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Conserved domains on  [gi|330443522|ref|NP_010959|]
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crossover junction endodeoxyribonuclease [Saccharomyces cerevisiae S288C]

Protein Classification

PIN_YEN1 and H3TH_YEN1 domain-containing protein( domain architecture ID 10177334)

PIN_YEN1 and H3TH_YEN1 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 2-275 4.91e-60

FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium thermophilum junction-resolving enzyme GEN1, and fungal homologs; Fungal Endonuclease 1 (YEN1 and GEN1, GEN1 is known as YEN1 in Saccharomyces cerevisiae) is a four-way (Holliday) junction resolvase. Members of this subgroup belong to 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: 350218 [Multi-domain]  Cd Length: 229  Bit Score: 202.50  E-value: 4.91e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522   2 GVSQIWEFLKPYLQDSRIPLRKFVIDFNKSQKRAPRIAIDAYGWLFECGFIQNidisarsrsrsrsptrsprdsdidssq 81
Cdd:cd09870    1 GIPGLWDLLEPAAESRSLAELAVVEEFNKRGGRPLRIGIDASIWLFHAQSSFG--------------------------- 53

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522  82 eyyGSRSYTTTGKAVINFISRLKELLSLNVEFLLVFDGVMKPSFKRKFNHEQnattcddekeyyssweqhvknhevygnc 161
Cdd:cd09870   54 ---GGHIQAGENPELRTLFYRLARLLSLPIQPVFVFDGPNRPPFKRGKKVGK---------------------------- 102

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522 162 kgllaPSDPEFISLVRKLLDLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKNYSKFYDDFGPSSI 241
Cdd:cd09870  103 -----STPHWLTKLFKELLDAFGFPWHEAPGEAEAELARLQRLGVVDAVLTDDSDALVFGATTVLRNFSKKLSDDDVKVY 177

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 330443522 242 TSHSPSRHHD---SKESFVTVIDLPKINKVAGKKFDR 275
Cdd:cd09870  178 TASAIKDKADltrTSLRGPREPDLPRLAALCEKYFSW 214
H3TH_YEN1 cd09906
H3TH domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' ...
 286-388 2.25e-31

H3TH domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease; Yeast Endonuclease 1 (YEN1): Holliday junction resolvase which promotes reciprocal exchange during mitotic recombination to maintain genome integrity in budding yeast. YEN1 is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of YEN1 and other similar fungal 5' nucleases. 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. These nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) 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 one Asp residue 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: 188626  Cd Length: 105  Bit Score: 118.18  E-value: 2.25e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522 286 GADYNR-GVKGLGKNKSLQLAQCEdpnFSMEFYDIFKDFNLEDLtseslrKSRYRLFQKRLYLYCKDHSVELFGRNYPVl 364
Cdd:cd09906   12 GGDYDTvGLPGCGKKTALELAKLG---FGDSLLEAAEDLSEEEL------ESFLEEWRERLLEELRTNGRGLFGRNYPA- 81

                         90       100
                 ....*....|....*....|....
gi 330443522 365 LNQGSFEGWPSTVAIMHYFHPIVQ 388
Cdd:cd09906   82 LSLSIPEGFPDPDVLLYYTHPVVS 105
 
Name Accession Description Interval E-value
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 2-275 4.91e-60

FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium thermophilum junction-resolving enzyme GEN1, and fungal homologs; Fungal Endonuclease 1 (YEN1 and GEN1, GEN1 is known as YEN1 in Saccharomyces cerevisiae) is a four-way (Holliday) junction resolvase. Members of this subgroup belong to 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: 350218 [Multi-domain]  Cd Length: 229  Bit Score: 202.50  E-value: 4.91e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522   2 GVSQIWEFLKPYLQDSRIPLRKFVIDFNKSQKRAPRIAIDAYGWLFECGFIQNidisarsrsrsrsptrsprdsdidssq 81
Cdd:cd09870    1 GIPGLWDLLEPAAESRSLAELAVVEEFNKRGGRPLRIGIDASIWLFHAQSSFG--------------------------- 53

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522  82 eyyGSRSYTTTGKAVINFISRLKELLSLNVEFLLVFDGVMKPSFKRKFNHEQnattcddekeyyssweqhvknhevygnc 161
Cdd:cd09870   54 ---GGHIQAGENPELRTLFYRLARLLSLPIQPVFVFDGPNRPPFKRGKKVGK---------------------------- 102

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522 162 kgllaPSDPEFISLVRKLLDLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKNYSKFYDDFGPSSI 241
Cdd:cd09870  103 -----STPHWLTKLFKELLDAFGFPWHEAPGEAEAELARLQRLGVVDAVLTDDSDALVFGATTVLRNFSKKLSDDDVKVY 177

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 330443522 242 TSHSPSRHHD---SKESFVTVIDLPKINKVAGKKFDR 275
Cdd:cd09870  178 TASAIKDKADltrTSLRGPREPDLPRLAALCEKYFSW 214
H3TH_YEN1 cd09906
H3TH domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' ...
 286-388 2.25e-31

H3TH domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease; Yeast Endonuclease 1 (YEN1): Holliday junction resolvase which promotes reciprocal exchange during mitotic recombination to maintain genome integrity in budding yeast. YEN1 is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of YEN1 and other similar fungal 5' nucleases. 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. These nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) 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 one Asp residue 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: 188626  Cd Length: 105  Bit Score: 118.18  E-value: 2.25e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522 286 GADYNR-GVKGLGKNKSLQLAQCEdpnFSMEFYDIFKDFNLEDLtseslrKSRYRLFQKRLYLYCKDHSVELFGRNYPVl 364
Cdd:cd09906   12 GGDYDTvGLPGCGKKTALELAKLG---FGDSLLEAAEDLSEEEL------ESFLEEWRERLLEELRTNGRGLFGRNYPA- 81

                         90       100
                 ....*....|....*....|....
gi 330443522 365 LNQGSFEGWPSTVAIMHYFHPIVQ 388
Cdd:cd09906   82 LSLSIPEGFPDPDVLLYYTHPVVS 105
XPGI smart00484
Xeroderma pigmentosum G I-region; domain in nucleases
 181-262 1.21e-21

Xeroderma pigmentosum G I-region; domain in nucleases


Pssm-ID: 214689 [Multi-domain]  Cd Length: 73  Bit Score: 89.18  E-value: 1.21e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522   181 DLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKNYSKFYDDFGPssitshspsRHHDSKESFVTVI 260
Cdd:smart00484   1 RLMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLE---------FRIIDLESVLKEL 71


                   ..
gi 330443522   261 DL 262
Cdd:smart00484  72 GL 73
XPG_I pfam00867
XPG I-region;
184-270 3.48e-21

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 88.34  E-value: 3.48e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522  184 NISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKNYSKFYDdfgpssitshspsrhhDSKESFVTVIDLP 263
Cdd:pfam00867   1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSK----------------KKSKVPVEEIDLE 64


                  ....*..
gi 330443522  264 KINKVAG 270
Cdd:pfam00867  65 KILKELG 71
PRK03980 PRK03980
flap endonuclease-1; Provisional
 169-304 1.81e-12

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 68.69  E-value: 1.81e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522 169 DPEFISLVRKLLDLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKNyskfyddfgpssITShSPSR 248
Cdd:PRK03980  81 TDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRN------------LTI-SGKR 147

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522 249 HHDSKESFVTV----IDLPKINKVAGkkFDRLSLLFFSVLLGADYNRGVKGLGKNKSLQL 304
Cdd:PRK03980 148 KLPGKNVYVEVkpelIELEEVLKELG--ITREQLIDIAILVGTDYNPGIKGIGPKTALKL 205
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 176-297 1.09e-06

DNA excision repair protein (rad2); All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273166 [Multi-domain]  Cd Length: 1034  Bit Score: 52.21  E-value: 1.09e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522   176 VRKLLDLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKNYskFyddfgpssitshspsrhhdSKES 255
Cdd:TIGR00600  777 SQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNF--F-------------------NQNK 835

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 330443522   256 FVTVIDLPKINKVAGkkFDRLSLLFFSVLLGADYNRGVKGLG 297
Cdd:TIGR00600  836 FVEYYQYVDIHNQLG--LDRNKLINLAYLLGSDYTEGIPTVG 875
 
Name Accession Description Interval E-value
PIN_YEN1 cd09870
FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium ...
 2-275 4.91e-60

FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium thermophilum junction-resolving enzyme GEN1, and fungal homologs; Fungal Endonuclease 1 (YEN1 and GEN1, GEN1 is known as YEN1 in Saccharomyces cerevisiae) is a four-way (Holliday) junction resolvase. Members of this subgroup belong to 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: 350218 [Multi-domain]  Cd Length: 229  Bit Score: 202.50  E-value: 4.91e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522   2 GVSQIWEFLKPYLQDSRIPLRKFVIDFNKSQKRAPRIAIDAYGWLFECGFIQNidisarsrsrsrsptrsprdsdidssq 81
Cdd:cd09870    1 GIPGLWDLLEPAAESRSLAELAVVEEFNKRGGRPLRIGIDASIWLFHAQSSFG--------------------------- 53

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522  82 eyyGSRSYTTTGKAVINFISRLKELLSLNVEFLLVFDGVMKPSFKRKFNHEQnattcddekeyyssweqhvknhevygnc 161
Cdd:cd09870   54 ---GGHIQAGENPELRTLFYRLARLLSLPIQPVFVFDGPNRPPFKRGKKVGK---------------------------- 102

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522 162 kgllaPSDPEFISLVRKLLDLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKNYSKFYDDFGPSSI 241
Cdd:cd09870  103 -----STPHWLTKLFKELLDAFGFPWHEAPGEAEAELARLQRLGVVDAVLTDDSDALVFGATTVLRNFSKKLSDDDVKVY 177

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 330443522 242 TSHSPSRHHD---SKESFVTVIDLPKINKVAGKKFDR 275
Cdd:cd09870  178 TASAIKDKADltrTSLRGPREPDLPRLAALCEKYFSW 214
H3TH_YEN1 cd09906
H3TH domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' ...
 286-388 2.25e-31

H3TH domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease; Yeast Endonuclease 1 (YEN1): Holliday junction resolvase which promotes reciprocal exchange during mitotic recombination to maintain genome integrity in budding yeast. YEN1 is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of YEN1 and other similar fungal 5' nucleases. 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. These nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) 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 one Asp residue 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: 188626  Cd Length: 105  Bit Score: 118.18  E-value: 2.25e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522 286 GADYNR-GVKGLGKNKSLQLAQCEdpnFSMEFYDIFKDFNLEDLtseslrKSRYRLFQKRLYLYCKDHSVELFGRNYPVl 364
Cdd:cd09906   12 GGDYDTvGLPGCGKKTALELAKLG---FGDSLLEAAEDLSEEEL------ESFLEEWRERLLEELRTNGRGLFGRNYPA- 81

                         90       100
                 ....*....|....*....|....
gi 330443522 365 LNQGSFEGWPSTVAIMHYFHPIVQ 388
Cdd:cd09906   82 LSLSIPEGFPDPDVLLYYTHPVVS 105
XPGI smart00484
Xeroderma pigmentosum G I-region; domain in nucleases
 181-262 1.21e-21

Xeroderma pigmentosum G I-region; domain in nucleases


Pssm-ID: 214689 [Multi-domain]  Cd Length: 73  Bit Score: 89.18  E-value: 1.21e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522   181 DLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKNYSKFYDDFGPssitshspsRHHDSKESFVTVI 260
Cdd:smart00484   1 RLMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLE---------FRIIDLESVLKEL 71


                   ..
gi 330443522   261 DL 262
Cdd:smart00484  72 GL 73
XPG_I pfam00867
XPG I-region;
184-270 3.48e-21

XPG I-region;


Pssm-ID: 459970 [Multi-domain]  Cd Length: 87  Bit Score: 88.34  E-value: 3.48e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522  184 NISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKNYSKFYDdfgpssitshspsrhhDSKESFVTVIDLP 263
Cdd:pfam00867   1 GIPYVVAPGEAEAQCAYLQKSGLVDAVISEDSDVLLFGAPRLLRNLTGKSK----------------KKSKVPVEEIDLE 64


                  ....*..
gi 330443522  264 KINKVAG 270
Cdd:pfam00867  65 KILKELG 71
PIN_XPG_RAD2 cd09868
FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a ...
 99-228 1.01e-15

FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member 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: 350216 [Multi-domain]  Cd Length: 209  Bit Score: 76.40  E-value: 1.01e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522  99 FISRLKELLSLNVEFLLVFDGVmKPSFKRKfnheqnatTCDdekeyysswEQHVKNHEVYGNCKgllapsdpefislvrK 178
Cdd:cd09868   57 FFRRICKLLFYGIKPVFVFDGP-APALKRR--------TLA---------RRRSVTDEMYEEIQ---------------E 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 330443522 179 LLDLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKN 228
Cdd:cd09868  104 LLRLFGIPYIVAPMEAEAQCAFLERLGLVDGVITDDSDVFLFGAKRVYKN 153
PIN_FEN1_EXO1-like cd00128
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like ...
 6-232 3.57e-15

FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like nucleases, structure-specific, divalent-metal-ion dependent, 5' nucleases; PIN (PilT N terminus) domain of Flap endonuclease-1 (FEN1) and exonuclease-1 (EXO1)-like nucleases: FEN1, EXO1, Mkt1, Gap endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. 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: 350200 [Multi-domain]  Cd Length: 162  Bit Score: 73.56  E-value: 3.57e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522   6 IWEFLKPYLQdsRIPLRKFvidFNKsqkrapRIAIDAYGWLFEcgFIQNIdisarsrsrsrsptrsprdsdidssQEYYG 85
Cdd:cd00128    1 LWQFIGEAKE--PISIESL---KGK------TVAIDASIWVYQ--FLTAK-------------------------REQGG 42

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522  86 SRSYTTTgkAVINFISRLKELLSLNVEFLLVFDGVMKPSFKRKFNHEqnattcddekeyyssweqhvknheVYGNCKgll 165
Cdd:cd00128   43 DIGVTNS--HLRGLFYRIIKLLSNGIKPIFVFDGGPPPLKKETITKK------------------------MYQECK--- 93

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 330443522 166 apsdpefislvrKLLDLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKNYSKF 232
Cdd:cd00128   94 ------------HLLSLFGIPYVVAPYEAEAQCAYLLKAGIVDAAITEDSDCLLFGAPRVIRNMTFE 148
PIN_EXO1 cd09857
FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' ...
 1-226 2.05e-14

FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; exonuclease-1 (EXO1) is involved in multiple, eukaryotic DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity), DNA repair processes (DNA mismatch repair (MMR) and post-replication repair (PRR)), recombination, and telomere integrity. EXO1 functions in the MMS2 error-free branch of the PRR pathway in the maintenance and repair of stalled replication forks. Studies also suggest that EXO1 plays both structural and catalytic roles during MMR-mediated mutation avoidance. 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. EXO1 nucleases also have C-terminal Mlh1- and Msh2-binding domains which allow interaction with MMR and PRR proteins, respectively.


Pssm-ID: 350207 [Multi-domain]  Cd Length: 202  Bit Score: 72.44  E-value: 2.05e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522   1 MGVSQIWEFLKPYLQDSRIplRKFvidfnksqkRAPRIAIDAYGWL----FECgfiqnidisarsrsrsrsptrsprdsd 76
Cdd:cd09857    1 MGIQGLLPFLKPIQRPVHI--SEY---------AGKTVAVDAYCWLhrgaYSC--------------------------- 42

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522  77 idsSQEYYGSRSyttTGKAVINFISRLKELLSLNVEFLLVFDGVMKPSfKRKFNHEQNATtcddEKEYYSSWEQHVKNH- 155
Cdd:cd09857   43 ---AEELALGKP---TDKYIDYCMKRVNMLLHHGITPILVFDGAPLPS-KAGTEEERRER----REEALEKALELLREGk 111

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 330443522 156 --EVYGNCKGLLAPSdPEFISLVRKLLDLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKIL 226
Cdd:cd09857  112 ksEARECFQRAVDIT-PEMAHELIKALRKENVEYIVAPYEADAQLAYLAKTGYVDAVITEDSDLLAFGCPKVL 183
PIN_FEN1-like cd09856
FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, ...
 5-230 1.10e-13

FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, divalent-metal-ion dependent, 5' nucleases; PIN (PilT N terminus) domain of Flap endonuclease-1 (FEN1)-like nucleases: FEN1, Gap endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Nucleases in this subfamily 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: 350206 [Multi-domain]  Cd Length: 235  Bit Score: 71.42  E-value: 1.10e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522   5 QIWEFLKPYLQdsRIPLRKFvidfnksqkRAPRIAIDAYGWLFEcgfiqnidisarsrsrsrsptrsprdsdIDSSQEYY 84
Cdd:cd09856    1 GFWKIIGPSKR--RISLESL---------RGKRVAIDASIWIYQ----------------------------FLTAVRGQ 41

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522  85 GSRSYTTTgkAVINFISRLKELLSLNVEFLLVFDGVMKPSFK---------RKFNHEQNATTCDDEKEYYSSWEQhvkNH 155
Cdd:cd09856   42 GGNGVSNS--HIRGLFYRIIRLLENGIKPVFVFDGEPPKLKKrtrrkrkerRQGAEESAKSAVEDELFEEQSKDK---KR 116

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 330443522 156 EVYGNckgllapsdPEFISLVRKLLDLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKNYS 230
Cdd:cd09856  117 SGTVT---------KVMTAECKHLLSLFGIPYVDAPGEAEAQCAYLEQQGIVDAVLTEDVDTFLFGSPVVYRNLT 182
PRK03980 PRK03980
flap endonuclease-1; Provisional
 169-304 1.81e-12

flap endonuclease-1; Provisional


Pssm-ID: 235185 [Multi-domain]  Cd Length: 292  Bit Score: 68.69  E-value: 1.81e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522 169 DPEFISLVRKLLDLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKNyskfyddfgpssITShSPSR 248
Cdd:PRK03980  81 TDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRN------------LTI-SGKR 147

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522 249 HHDSKESFVTV----IDLPKINKVAGkkFDRLSLLFFSVLLGADYNRGVKGLGKNKSLQL 304
Cdd:PRK03980 148 KLPGKNVYVEVkpelIELEEVLKELG--ITREQLIDIAILVGTDYNPGIKGIGPKTALKL 205
PIN_GEN1 cd09869
FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, ...
 98-230 1.23e-11

FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; Gap Endonuclease 1 (GEN1) is a Holliday junction resolvase reported to symmetrically cleave Holliday junctions and allow religation without additional processing. GEN1 is a member 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: 350217 [Multi-domain]  Cd Length: 227  Bit Score: 64.93  E-value: 1.23e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522  98 NFISRLKELLSLNVEFLLVFDGVmKPSFKRkfnheqnattcddekEYYSSweqhvKNHEVYGNCKGLLAPSD---PEFIS 174
Cdd:cd09869   54 NLFFRTVNLLRLGIKPVFVLDGD-APELKL---------------QTIKK-----RNAARFGGAKKKGGSKKrgrSRFSR 112

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 330443522 175 LVRK---LLDLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKNYS 230
Cdd:cd09869  113 VLKEceeLLELLGVPVVQAPGEAEALCALLNAEGLVDGCITNDGDAFLYGARTVYRNFS 171
PIN_FEN1 cd09867
FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion ...
 169-228 5.96e-10

FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; Flap endonuclease-1 (FEN1) is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. FEN1 belongs to the FEN1-EXO1-like subfamily of structure-specific, 5' nucleases (FEN-like family). 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. FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA.


Pssm-ID: 350215 [Multi-domain]  Cd Length: 251  Bit Score: 60.49  E-value: 5.96e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522 169 DPEFISLVRKLLDLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKN 228
Cdd:cd09867  126 TKEMVEEAKKLLDLMGIPYVQAPSEGEAQAAYLVKKGDVYAVASQDYDSLLFGAPRLVRN 185
PTZ00217 PTZ00217
flap endonuclease-1; Provisional
 176-228 1.18e-07

flap endonuclease-1; Provisional


Pssm-ID: 240317 [Multi-domain]  Cd Length: 393  Bit Score: 54.63  E-value: 1.18e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 330443522 176 VRKLLDLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKN 228
Cdd:PTZ00217 143 AKKLLRLMGIPVIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRN 195
rad2 TIGR00600
DNA excision repair protein (rad2); All proteins in this family for which functions are known ...
 176-297 1.09e-06

DNA excision repair protein (rad2); All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273166 [Multi-domain]  Cd Length: 1034  Bit Score: 52.21  E-value: 1.09e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522   176 VRKLLDLMNISYVIACGEGEAQCVWLQVSGAVDFILSNDSDTLVFGGEKILKNYskFyddfgpssitshspsrhhdSKES 255
Cdd:TIGR00600  777 SQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNF--F-------------------NQNK 835

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 330443522   256 FVTVIDLPKINKVAGkkFDRLSLLFFSVLLGADYNRGVKGLG 297
Cdd:TIGR00600  836 FVEYYQYVDIHNQLG--LDRNKLINLAYLLGSDYTEGIPTVG 875
XPGN smart00485
Xeroderma pigmentosum G N-region; domain in nucleases
 1-128 3.64e-05

Xeroderma pigmentosum G N-region; domain in nucleases


Pssm-ID: 214690 [Multi-domain]  Cd Length: 99  Bit Score: 42.99  E-value: 3.64e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 330443522     1 MGVSQIWEFLKPYLqdSRIPLRKFvidfnksqkRAPRIAIDAYGWLFEcgFIQNIdisarsrsrsrsptrsprdsdidsS 80
Cdd:smart00485   1 MGIKGLWPLLKPVV--REVPLEAL---------RGKTLAIDASIWLYQ--FLTAC------------------------R 43

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 330443522    81 QEYYGSrsyTTTGKAVINFISRLKELLSLNVEFLLVFDGVmKPSFKRK 128
Cdd:smart00485  44 EKLGTP---LPNSKHLMGLFYRTCRLLEFGIKPIFVFDGK-PPPLKSE 87
H3TH_XPG-like cd09900
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 ...
 286-318 7.38e-05

H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (archaeal), GEN1, YEN1, and XPG; The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of archaeal Flap Endonuclease-1 (FEN1), Gap Endonuclease 1 (GEN1), Yeast Endonuclease 1 (YEN1), Xeroderma pigmentosum complementation group G (XPG) nuclease, and other eukaryotic and archaeal homologs. 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. With the except of the Mkt1-like proteins, the nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) 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 one Asp residue 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: 188620 [Multi-domain]  Cd Length: 52  Bit Score: 40.93  E-value: 7.38e-05
                         10        20        30
                 ....*....|....*....|....*....|...
gi 330443522 286 GADYNRGVKGLGKNKSLQLAQCEdPNFSMEFYD 318
Cdd:cd09900   11 GTDYNPGVPGIGPKTALELLKEF-GEDLEKFLE 42
 
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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