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Conserved domains on  [gi|755446323|gb|AJK10332|]
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hypothetical protein CH60_4215 (plasmid) [Yersinia pestis str. Pestoides B]

Protein Classification

PIN domain nuclease; PIN domain-containing protein( domain architecture ID 10177216)

PIN domain nuclease similar to Enterobacteria phage exodeoxyribonuclease that is essential for phage DNA replication| PIN (PilT N terminus) domain-containing protein may function as a nuclease

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_T4-like cd09860
FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N ...
 3-157 6.18e-68

FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N terminus) domain of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, metal binding site 1, whereas exonuclease activity requires both, the high-affinity, metal binding site 1 and the low-affinity, metal binding site 2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors.


:

Pssm-ID: 350210  Cd Length: 158  Bit Score: 208.98  E-value: 6.18e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323   3 YLFVDGNSLGYYHQQSDKLHNGEMEVQAAFGFVKNVRRYASIL-HARPMILWDGFSDKRRDFYPEYKANRDDDP-DMKKM 80
Cdd:cd09860    1 LLLIDGNSIGFAAQHSAKLTAGGMEVQARFGFLRSIRSYLKRYkYAKPIVLWDGRASWRKDLFPEYKANRKKTReEKKAW 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 755446323  81 KEGFAIQKPYILKMMTALGVNQLIAKDAEADDLAGMLVSRLAPQptVDHIYLLTGDGDWLQLVRENVSWVSLREDAK 157
Cdd:cd09860   81 REAFEAQRPFIEEALEYLGVPQIRAPGAEADDLAGVLVKRLAAF--GDKVLLVSGDKDWLQLVYENVSWFSPITDKE 155
H3TH_T4-like cd09899
H3TH domain of bacteriophage T3, T4 RNase H, T5-5' nucleases, and homologs; H3TH ...
 174-264 5.02e-15

H3TH domain of bacteriophage T3, T4 RNase H, T5-5' nucleases, and homologs; H3TH (helix-3-turn-helix) domains of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. The T5-5'nuclease is a 5'-3' exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3' exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. These nucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. They contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors required for nuclease activity. The first metal binding site (MBS-1) is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site (MBS-2) is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, MBS-1, whereas exonuclease activity requires both, the high-affinity, MBS-1 and the low-affinity, MBS-2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases.


:

Pssm-ID: 188619 [Multi-domain]  Cd Length: 74  Bit Score: 68.68  E-value: 5.02e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323 174 TPRAFLEAKALQGDTSDNIKGVGGIGDGGAKELLHEWGSVAAMVRGINDGSIVInkgryktafnklaknafNEKTGCRML 253
Cdd:cd09899    1 DPEAYLSAKALAGDTKDNIAGVPGIGTGRATKLLEEIGDVADIIDALLTPGKVK-----------------NSLALEEAY 63

                         90
                 ....*....|.
gi 755446323 254 EAFKRNMMLMN 264
Cdd:cd09899   64 ERFKENLILID 74
 
Name Accession Description Interval E-value
PIN_T4-like cd09860
FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N ...
 3-157 6.18e-68

FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N terminus) domain of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, metal binding site 1, whereas exonuclease activity requires both, the high-affinity, metal binding site 1 and the low-affinity, metal binding site 2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors.


Pssm-ID: 350210  Cd Length: 158  Bit Score: 208.98  E-value: 6.18e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323   3 YLFVDGNSLGYYHQQSDKLHNGEMEVQAAFGFVKNVRRYASIL-HARPMILWDGFSDKRRDFYPEYKANRDDDP-DMKKM 80
Cdd:cd09860    1 LLLIDGNSIGFAAQHSAKLTAGGMEVQARFGFLRSIRSYLKRYkYAKPIVLWDGRASWRKDLFPEYKANRKKTReEKKAW 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 755446323  81 KEGFAIQKPYILKMMTALGVNQLIAKDAEADDLAGMLVSRLAPQptVDHIYLLTGDGDWLQLVRENVSWVSLREDAK 157
Cdd:cd09860   81 REAFEAQRPFIEEALEYLGVPQIRAPGAEADDLAGVLVKRLAAF--GDKVLLVSGDKDWLQLVYENVSWFSPITDKE 155
53EXOc smart00475
5'-3' exonuclease;
4-279 1.09e-64

5'-3' exonuclease;


Pssm-ID: 214682 [Multi-domain]  Cd Length: 259  Bit Score: 204.37  E-value: 1.09e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323     4 LFVDGNSLGY--YHQQSD-KLHNGEMeVQAAFGFVKNVRRYASILH-ARPMILWD-GFSDKRRDFYPEYKANRDddpdmk 78
Cdd:smart00475   4 LLVDGSSLAFraYFALPPlKNSKGEP-TNAVYGFLRMLLKLIKEEKpTYVAVVFDaKGKTFRHELYPEYKANRP------ 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323    79 KMKEGFAIQKPYILKMMTALGVNQLIAKDAEADDLAGMLVSRLAPqpTVDHIYLLTGDGDWLQLVRENVS-WVSLREDAK 157
Cdd:smart00475  77 KTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEA--EGYEVRIVSGDKDLLQLVSDKVSvLDPTKGIKE 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323   158 HKQVNFEQFAELTGLpTPRAFLEAKALQGDTSDNIKGVGGIGDGGAKELLHEWGSVAAMVRGINDgsivinkgryktafn 237
Cdd:smart00475 155 FELYTPENVIEKYGL-TPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLDK--------------- 218

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|...
gi 755446323   238 klAKNAFNEKTGCRMlEAFKRNMMLMNlIDTKFP-PSEIESIK 279
Cdd:smart00475 219 --LKKKLREKLLAHK-EDAKLSRKLAT-IETDVPlEVDLEDLR 257
ExoIX COG0258
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];
4-303 2.12e-39

5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];


Pssm-ID: 440028 [Multi-domain]  Cd Length: 286  Bit Score: 139.78  E-value: 2.12e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323   4 LFVDGNSLGY--YHQQSDkLHNGE-MEVQAAFGFVKNVRRYASILHARPM-ILWD-GFSDKRRDFYPEYKANRdddpdmK 78
Cdd:COG0258    8 LLIDGSSLLFraFYALPP-LTNSDgQPTNAVYGFTNMLLKLLKEEKPTHLaVAFDaKGPTFRHELYPEYKANR------P 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323  79 KMKEGFAIQKPYILKMMTALGVNQLIAKDAEADDLAGMLVSRLAPQPtvDHIYLLTGDGDWLQLVRENVSWVSL-REDAK 157
Cdd:COG0258   81 EMPEELRPQIPLIKEVLEALGIPVLEVEGYEADDVIGTLAKQAEAEG--YEVLIVTGDKDLLQLVDDNVTVLDPmKGVSE 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323 158 HKQVNFEQFAELTGLPtPRAFLEAKALQGDTSDNI--------KgvggigdgGAKELLHEWGSVAAMVRGINDgsIvinK 229
Cdd:COG0258  159 LERYDPAEVEEKYGVP-PEQIIDYLALMGDSSDNIpgvpgigeK--------TAAKLLQEYGSLENILANADE--I---K 224

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 755446323 230 GRYKTAFNKLAKNAFnektGCRMLEAFKRNMMLmnlidtkfpPSEIESIK-GARDMNAFEQMCCELNFRSFLEDL 303
Cdd:COG0258  225 GKLREKLRENKEQAR----LSRKLATIKTDVPL---------PFDLEDLKlRPPDREALRELFEELEFKSLLKRL 286
5_3_exonuc_N pfam02739
5'-3' exonuclease, N-terminal resolvase-like domain;
4-148 2.83e-27

5'-3' exonuclease, N-terminal resolvase-like domain;


Pssm-ID: 460672  Cd Length: 163  Bit Score: 104.40  E-value: 2.83e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323    4 LFVDGNSL---GYYHQQSDKLHNGeMEVQAAFGFVKNVRRYASILHARPM-ILWDGFSDKRRDFYPEYKANRdddpdmKK 79
Cdd:pfam02739   3 LLIDGSSLlfrAFYALPPLTNSDG-LPTNAVYGFLNMLLKLLKEEKPTHVaVAFDAKPTFRHELYPEYKANR------PP 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755446323   80 MKEGFAIQKPYILKMMTALGVNQLIAKDAEADDLAGMLVSRLAPQptVDHIYLLTGDGDWLQLVRENVS 148
Cdd:pfam02739  76 MPEELRPQIPLIKELLEALGIPVLEVEGYEADDIIGTLAKRAEEE--GYEVVIVTGDKDLLQLVSDNVT 142
PRK05755 PRK05755
DNA polymerase I; Provisional
 1-213 1.88e-21

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 94.77  E-value: 1.88e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323   1 MNYLF-VDGNSLGY--YHQQSDKLHNGE-MEVQAAFGFVKNVRRYASILHARPM-ILWDG----FsdkRRDFYPEYKANR 71
Cdd:PRK05755   1 MKTLLlIDGSSLLFraFYALLPTLRNSDgLPTGAVYGFLNMLLKLLKEEKPTHVaVAFDAkgktF---RHELYPEYKANR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323  72 DddpdmkKMKEGFAIQKPYILKMMTALGVNQLIAKDAEADDLAGMLvSRLAPQPTVDhIYLLTGDGDWLQLVRENVSWVS 151
Cdd:PRK05755  78 P------PMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTL-AKQAEAAGYE-VLIVTGDKDLLQLVDDNVTLLD 149

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323 152 LREDAKHKQVNFEQFAELTGLpTPRAFLEAKALQGDTSDNI--------KgvggigdgGAKELLHEWGSV 213
Cdd:PRK05755 150 TMGVSKNEELDPEEVVEKYGV-TPEQIIDYLALMGDSSDNIpgvpgigeK--------TAAKLLQEYGSL 210
H3TH_T4-like cd09899
H3TH domain of bacteriophage T3, T4 RNase H, T5-5' nucleases, and homologs; H3TH ...
 174-264 5.02e-15

H3TH domain of bacteriophage T3, T4 RNase H, T5-5' nucleases, and homologs; H3TH (helix-3-turn-helix) domains of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. The T5-5'nuclease is a 5'-3' exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3' exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. These nucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. They contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors required for nuclease activity. The first metal binding site (MBS-1) is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site (MBS-2) is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, MBS-1, whereas exonuclease activity requires both, the high-affinity, MBS-1 and the low-affinity, MBS-2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases.


Pssm-ID: 188619 [Multi-domain]  Cd Length: 74  Bit Score: 68.68  E-value: 5.02e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323 174 TPRAFLEAKALQGDTSDNIKGVGGIGDGGAKELLHEWGSVAAMVRGINDGSIVInkgryktafnklaknafNEKTGCRML 253
Cdd:cd09899    1 DPEAYLSAKALAGDTKDNIAGVPGIGTGRATKLLEEIGDVADIIDALLTPGKVK-----------------NSLALEEAY 63

                         90
                 ....*....|.
gi 755446323 254 EAFKRNMMLMN 264
Cdd:cd09899   64 ERFKENLILID 74
5_3_exonuc pfam01367
5'-3' exonuclease, C-terminal SAM fold;
174-244 3.03e-04

5'-3' exonuclease, C-terminal SAM fold;


Pssm-ID: 460176 [Multi-domain]  Cd Length: 93  Bit Score: 39.27  E-value: 3.03e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755446323  174 TPRAFLEAKALQGDTSDNI--------KgvggigdgGAKELLHEWGSVAAMVRGINDgsivINKGRYKTAFNKLAKNAF 244
Cdd:pfam01367   2 TPEQIIDYLALMGDSSDNIpgvpgigeK--------TAAKLLNEYGSLENILANADE----IKGGKLREKLRENKEQAL 68
 
Name Accession Description Interval E-value
PIN_T4-like cd09860
FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N ...
 3-157 6.18e-68

FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N terminus) domain of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, metal binding site 1, whereas exonuclease activity requires both, the high-affinity, metal binding site 1 and the low-affinity, metal binding site 2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors.


Pssm-ID: 350210  Cd Length: 158  Bit Score: 208.98  E-value: 6.18e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323   3 YLFVDGNSLGYYHQQSDKLHNGEMEVQAAFGFVKNVRRYASIL-HARPMILWDGFSDKRRDFYPEYKANRDDDP-DMKKM 80
Cdd:cd09860    1 LLLIDGNSIGFAAQHSAKLTAGGMEVQARFGFLRSIRSYLKRYkYAKPIVLWDGRASWRKDLFPEYKANRKKTReEKKAW 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 755446323  81 KEGFAIQKPYILKMMTALGVNQLIAKDAEADDLAGMLVSRLAPQptVDHIYLLTGDGDWLQLVRENVSWVSLREDAK 157
Cdd:cd09860   81 REAFEAQRPFIEEALEYLGVPQIRAPGAEADDLAGVLVKRLAAF--GDKVLLVSGDKDWLQLVYENVSWFSPITDKE 155
53EXOc smart00475
5'-3' exonuclease;
4-279 1.09e-64

5'-3' exonuclease;


Pssm-ID: 214682 [Multi-domain]  Cd Length: 259  Bit Score: 204.37  E-value: 1.09e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323     4 LFVDGNSLGY--YHQQSD-KLHNGEMeVQAAFGFVKNVRRYASILH-ARPMILWD-GFSDKRRDFYPEYKANRDddpdmk 78
Cdd:smart00475   4 LLVDGSSLAFraYFALPPlKNSKGEP-TNAVYGFLRMLLKLIKEEKpTYVAVVFDaKGKTFRHELYPEYKANRP------ 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323    79 KMKEGFAIQKPYILKMMTALGVNQLIAKDAEADDLAGMLVSRLAPqpTVDHIYLLTGDGDWLQLVRENVS-WVSLREDAK 157
Cdd:smart00475  77 KTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEA--EGYEVRIVSGDKDLLQLVSDKVSvLDPTKGIKE 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323   158 HKQVNFEQFAELTGLpTPRAFLEAKALQGDTSDNIKGVGGIGDGGAKELLHEWGSVAAMVRGINDgsivinkgryktafn 237
Cdd:smart00475 155 FELYTPENVIEKYGL-TPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLDK--------------- 218

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|...
gi 755446323   238 klAKNAFNEKTGCRMlEAFKRNMMLMNlIDTKFP-PSEIESIK 279
Cdd:smart00475 219 --LKKKLREKLLAHK-EDAKLSRKLAT-IETDVPlEVDLEDLR 257
ExoIX COG0258
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];
4-303 2.12e-39

5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair];


Pssm-ID: 440028 [Multi-domain]  Cd Length: 286  Bit Score: 139.78  E-value: 2.12e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323   4 LFVDGNSLGY--YHQQSDkLHNGE-MEVQAAFGFVKNVRRYASILHARPM-ILWD-GFSDKRRDFYPEYKANRdddpdmK 78
Cdd:COG0258    8 LLIDGSSLLFraFYALPP-LTNSDgQPTNAVYGFTNMLLKLLKEEKPTHLaVAFDaKGPTFRHELYPEYKANR------P 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323  79 KMKEGFAIQKPYILKMMTALGVNQLIAKDAEADDLAGMLVSRLAPQPtvDHIYLLTGDGDWLQLVRENVSWVSL-REDAK 157
Cdd:COG0258   81 EMPEELRPQIPLIKEVLEALGIPVLEVEGYEADDVIGTLAKQAEAEG--YEVLIVTGDKDLLQLVDDNVTVLDPmKGVSE 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323 158 HKQVNFEQFAELTGLPtPRAFLEAKALQGDTSDNI--------KgvggigdgGAKELLHEWGSVAAMVRGINDgsIvinK 229
Cdd:COG0258  159 LERYDPAEVEEKYGVP-PEQIIDYLALMGDSSDNIpgvpgigeK--------TAAKLLQEYGSLENILANADE--I---K 224

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 755446323 230 GRYKTAFNKLAKNAFnektGCRMLEAFKRNMMLmnlidtkfpPSEIESIK-GARDMNAFEQMCCELNFRSFLEDL 303
Cdd:COG0258  225 GKLREKLRENKEQAR----LSRKLATIKTDVPL---------PFDLEDLKlRPPDREALRELFEELEFKSLLKRL 286
5_3_exonuc_N pfam02739
5'-3' exonuclease, N-terminal resolvase-like domain;
4-148 2.83e-27

5'-3' exonuclease, N-terminal resolvase-like domain;


Pssm-ID: 460672  Cd Length: 163  Bit Score: 104.40  E-value: 2.83e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323    4 LFVDGNSL---GYYHQQSDKLHNGeMEVQAAFGFVKNVRRYASILHARPM-ILWDGFSDKRRDFYPEYKANRdddpdmKK 79
Cdd:pfam02739   3 LLIDGSSLlfrAFYALPPLTNSDG-LPTNAVYGFLNMLLKLLKEEKPTHVaVAFDAKPTFRHELYPEYKANR------PP 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755446323   80 MKEGFAIQKPYILKMMTALGVNQLIAKDAEADDLAGMLVSRLAPQptVDHIYLLTGDGDWLQLVRENVS 148
Cdd:pfam02739  76 MPEELRPQIPLIKELLEALGIPVLEVEGYEADDIIGTLAKRAEEE--GYEVVIVTGDKDLLQLVSDNVT 142
PRK05755 PRK05755
DNA polymerase I; Provisional
 1-213 1.88e-21

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 94.77  E-value: 1.88e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323   1 MNYLF-VDGNSLGY--YHQQSDKLHNGE-MEVQAAFGFVKNVRRYASILHARPM-ILWDG----FsdkRRDFYPEYKANR 71
Cdd:PRK05755   1 MKTLLlIDGSSLLFraFYALLPTLRNSDgLPTGAVYGFLNMLLKLLKEEKPTHVaVAFDAkgktF---RHELYPEYKANR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323  72 DddpdmkKMKEGFAIQKPYILKMMTALGVNQLIAKDAEADDLAGMLvSRLAPQPTVDhIYLLTGDGDWLQLVRENVSWVS 151
Cdd:PRK05755  78 P------PMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTL-AKQAEAAGYE-VLIVTGDKDLLQLVDDNVTLLD 149

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323 152 LREDAKHKQVNFEQFAELTGLpTPRAFLEAKALQGDTSDNI--------KgvggigdgGAKELLHEWGSV 213
Cdd:PRK05755 150 TMGVSKNEELDPEEVVEKYGV-TPEQIIDYLALMGDSSDNIpgvpgigeK--------TAAKLLQEYGSL 210
PIN_53EXO cd09859
FEN-like PIN domains of PIN domain of the 5'-3' exonuclease of Thermus aquaticus DNA ...
 6-168 5.69e-21

FEN-like PIN domains of PIN domain of the 5'-3' exonuclease of Thermus aquaticus DNA polymerase I (Taq) and homologs; The 5'-3' exonuclease (53EXO) PIN (PilT N terminus) domain of multi-domain DNA polymerase I and single domain protein homologs are included in this family. Taq contains a polymerase domain for synthesizing a new DNA strand and a 53EXO PIN domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO PIN domain recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO PIN domain cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350209  Cd Length: 160  Bit Score: 87.42  E-value: 5.69e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323   6 VDGNSL---GYYHQQSDKLHNGEMeVQAAFGFVKNVRRyasILHARP----MILWDG----FsdkRRDFYPEYKANRddd 74
Cdd:cd09859    2 IDGSSLlyrAYYALPPLTTSDGEP-TNAVYGFTNMLLK---LLKEEKpdyiAVAFDAkgptF---RHELYPEYKANR--- 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323  75 pdmKKMKEGFAIQKPYILKMMTALGVNQLIAKDAEADDLAGMLVSRLAPQptVDHIYLLTGDGDWLQLVRENVSWVSLRE 154
Cdd:cd09859   72 ---PPMPEELIPQIPLIKELLEALGIPVLEVEGYEADDIIGTLAKKAEKE--GLEVVIVTGDKDLLQLVDDNVKVLDPKK 146

                        170
                 ....*....|....
gi 755446323 155 DAKHKQVNFEQFAE 168
Cdd:cd09859  147 GSKTEIYDEEEVKE 160
PRK14976 PRK14976
5'-3' exonuclease; Provisional
 2-212 1.44e-20

5'-3' exonuclease; Provisional


Pssm-ID: 237877 [Multi-domain]  Cd Length: 281  Bit Score: 89.24  E-value: 1.44e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323   2 NYLFVDGNSL-------GYYHQQSDKLHNGEMEVqAAFGFVKNVR------RYASILharpmILWD-GFSDKRRDFYPEY 67
Cdd:PRK14976   4 KALLIDGNSLifrsyyaTLKQGPKLKNNKGLPTN-AIHTFLTMIFkilkklNPSYIL-----IAFDaGRKTFRHQLYDEY 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323  68 KANRdddpdmKKMKEGFAIQKPYILKMMTALGVNQLIAKDAEADDLAGMLVSRLAPQPTVDHIYllTGDGDWLQLVRENV 147
Cdd:PRK14976  78 KQGR------KKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIY--SSDKDLLQLVNENT 149

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 755446323 148 SWVSLREDAKHKQVNFEQFAELTGLpTPRAFLEAKALQGDTSDNIKGVGGIGDGGAKELLHEWGS 212
Cdd:PRK14976 150 DVLLKKKGTSHFILNTNNFFELYGI-EPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGN 213
H3TH_T4-like cd09899
H3TH domain of bacteriophage T3, T4 RNase H, T5-5' nucleases, and homologs; H3TH ...
 174-264 5.02e-15

H3TH domain of bacteriophage T3, T4 RNase H, T5-5' nucleases, and homologs; H3TH (helix-3-turn-helix) domains of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. The T5-5'nuclease is a 5'-3' exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3' exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. These nucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. They contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors required for nuclease activity. The first metal binding site (MBS-1) is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site (MBS-2) is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, MBS-1, whereas exonuclease activity requires both, the high-affinity, MBS-1 and the low-affinity, MBS-2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases.


Pssm-ID: 188619 [Multi-domain]  Cd Length: 74  Bit Score: 68.68  E-value: 5.02e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323 174 TPRAFLEAKALQGDTSDNIKGVGGIGDGGAKELLHEWGSVAAMVRGINDGSIVInkgryktafnklaknafNEKTGCRML 253
Cdd:cd09899    1 DPEAYLSAKALAGDTKDNIAGVPGIGTGRATKLLEEIGDVADIIDALLTPGKVK-----------------NSLALEEAY 63

                         90
                 ....*....|.
gi 755446323 254 EAFKRNMMLMN 264
Cdd:cd09899   64 ERFKENLILID 74
PIN_53EXO-like cd00008
FEN-like PIN domains of the 5'-3' exonucleases of DNA polymerase I, bacteriophage T4 RNase H ...
 6-148 1.44e-13

FEN-like PIN domains of the 5'-3' exonucleases of DNA polymerase I, bacteriophage T4 RNase H and T5-5' nucleases, and homologs; PIN (PilT N terminus) domains of the 5'-3' exonucleases (53EXO) of multi-domain DNA polymerase I and single domain protein homologs, as well as, the PIN domains of bacteriophage T5-5'nuclease (T5FEN or 5'-3'exonuclease), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar nucleases are included in this family. The 53EXO of DNA polymerase I recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350199  Cd Length: 158  Bit Score: 67.28  E-value: 1.44e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323   6 VDGNSLGY--YHQQSDKLHNGEMeVQAAFGFVKNVRRYASILHARPMILW--DGFSDKRRDFYPEYKANRDDDPDMKK-M 80
Cdd:cd00008    2 VDGHHLAYrtFHANKGLTTSGEP-VQAVYGFAKSILKALKEDSGDAVIVVfdAKKPSFRHEAYGGYKANRAEKYAEEKpT 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755446323  81 KEGFAIQKPYILKMMTALGVNQLIAKDAEADDLAGMLVSRLAPQptVDHIYLLTGDGDWLQLVRENVS 148
Cdd:cd00008   81 PEDFFEQLALIKELVKLLGLARLEIPGYEADDVLASLVKKAEKE--GYEVRIISADGDLYQLLSDRVH 146
rnh PHA02567
RnaseH; Provisional
 60-192 1.31e-05

RnaseH; Provisional


Pssm-ID: 222882 [Multi-domain]  Cd Length: 304  Bit Score: 46.20  E-value: 1.31e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755446323  60 RRDFYPEYKANRDDDPD------------MKKMKEGFAIQKPYilKMMTALGvnqliakdAEADDLAGMLVSRLAPQptv 127
Cdd:PHA02567  79 RRDIAWYYKKNRKKDREespwdweglfeaINKIVDEIKENMPY--KVMKIDK--------AEADDIIAVLTKKFSAE--- 145

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 755446323 128 DH-IYLLTGDGDWLQLvrenvswvslredakHKQVNFEQFAELT------GLPTPRAFLEAKALQGDTSDNI 192
Cdd:PHA02567 146 GRpVLIVSSDGDFTQL---------------HKYPGVKQWSPMQkkwvkpKYGSPEKDLMTKIIKGDKKDGV 202
5_3_exonuc pfam01367
5'-3' exonuclease, C-terminal SAM fold;
174-244 3.03e-04

5'-3' exonuclease, C-terminal SAM fold;


Pssm-ID: 460176 [Multi-domain]  Cd Length: 93  Bit Score: 39.27  E-value: 3.03e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755446323  174 TPRAFLEAKALQGDTSDNI--------KgvggigdgGAKELLHEWGSVAAMVRGINDgsivINKGRYKTAFNKLAKNAF 244
Cdd:pfam01367   2 TPEQIIDYLALMGDSSDNIpgvpgigeK--------TAAKLLNEYGSLENILANADE----IKGGKLREKLRENKEQAL 68
H3TH_53EXO cd09898
H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; H3TH ...
 175-244 2.94e-03

H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; H3TH (helix-3-turn-helix) domains of the 5'-3' exonuclease (53EXO) of mutli-domain DNA polymerase I and single domain protein homologs are included in this family. Taq DNA polymerase I contains a polymerase domain for synthesizing a new DNA strand and a 53EXO domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+ or Mn2+ or Zn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases.


Pssm-ID: 188618 [Multi-domain]  Cd Length: 73  Bit Score: 35.84  E-value: 2.94e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755446323 175 PRAFLEAKALQGDTSDNI--------KgvggigdgGAKELLHEWGSVAAMVRGINdgsivINKGRYKTAFNKLAKNAF 244
Cdd:cd09898    1 PEQIIDYLALVGDSSDNIpgvpgigpK--------TAAKLLQEYGSLENILANLD-----ELKGKLREKLEENKEQAL 65
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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