5'-3' exonuclease;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186488278    73 KRVFFLDVSPLCYE----------GNKPSSQA---FGHWISLFFSQVSLTDPVIAVIDGeeGNQRRRELLPSYKAHRKSP 139
Cdd:smart00475   1 KKLLLVDGSSLAFRayfalpplknSKGEPTNAvygFLRMLLKLIKEEKPTYVAVVFDAK--GKTFRHELYPEYKANRPKT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186488278   140 NHGRYSKRPhqFVDEVLRKCNVPVVRIEGHEADDVVATLMEQAVQRGYRAVIASPDKDFKQLISENVQIVIPLADLRRWS 219
Cdd:smart00475  79 PDELLEQIP--LIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFE 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186488278   220 FYTLKHYHAQYNCDPQSDLSFRCIMGDEVDGVPGiqhmVPAFGRKTAMKLVRKHGSLESLLsaAAVRTVgRPYAQEALTK 299
Cdd:smart00475 157 LYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPG----VPGIGEKTAAKLLKEFGSLENIL--ENLDKL-KKKLREKLLA 229

                          250       260
                   ....*....|....*....|..
gi 186488278   300 YADYLRRNYQVLALNRDVRVQI 321
Cdd:smart00475 230 HKEDAKLSRKLATIETDVPLEV 251

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186488278 110 DPVIAVIDGEEGNqRRRELLPSYKAHRKSPnhgryskrP----HQF--VDEVLRKCNVPVVRIEGHEADDVVATLMEQAV 183
Cdd:cd09859   46 DYIAVAFDAKGPT-FRHELYPEYKANRPPM--------PeeliPQIplIKELLEALGIPVLEVEGYEADDIIGTLAKKAE 116

                         90       100
                 ....*....|....*....|....*...
gi 186488278 184 QRGYRAVIASPDKDFKQLISENVQIVIP 211
Cdd:cd09859  117 KEGLEVVIVTGDKDLLQLVDDNVKVLDP 144

5'-3' exonuclease;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186488278    73 KRVFFLDVSPLCYE----------GNKPSSQA---FGHWISLFFSQVSLTDPVIAVIDGeeGNQRRRELLPSYKAHRKSP 139
Cdd:smart00475   1 KKLLLVDGSSLAFRayfalpplknSKGEPTNAvygFLRMLLKLIKEEKPTYVAVVFDAK--GKTFRHELYPEYKANRPKT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186488278   140 NHGRYSKRPhqFVDEVLRKCNVPVVRIEGHEADDVVATLMEQAVQRGYRAVIASPDKDFKQLISENVQIVIPLADLRRWS 219
Cdd:smart00475  79 PDELLEQIP--LIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFE 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186488278   220 FYTLKHYHAQYNCDPQSDLSFRCIMGDEVDGVPGiqhmVPAFGRKTAMKLVRKHGSLESLLsaAAVRTVgRPYAQEALTK 299
Cdd:smart00475 157 LYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPG----VPGIGEKTAAKLLKEFGSLENIL--ENLDKL-KKKLREKLLA 229

                          250       260
                   ....*....|....*....|..
gi 186488278   300 YADYLRRNYQVLALNRDVRVQI 321
Cdd:smart00475 230 HKEDAKLSRKLATIETDVPLEV 251

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186488278 110 DPVIAVIDGEEGNqRRRELLPSYKAHRKSPnhgryskrP----HQF--VDEVLRKCNVPVVRIEGHEADDVVATLMEQAV 183
Cdd:cd09859   46 DYIAVAFDAKGPT-FRHELYPEYKANRPPM--------PeeliPQIplIKELLEALGIPVLEVEGYEADDIIGTLAKKAE 116

                         90       100
                 ....*....|....*....|....*...
gi 186488278 184 QRGYRAVIASPDKDFKQLISENVQIVIP 211
Cdd:cd09859  117 KEGLEVVIVTGDKDLLQLVDDNVKVLDP 144

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186488278 112 VIAVIDGeeGNQRRRELLPSYKAHRKSPnhgRYSKRP--------HQFVDEVLRKCNVPVVRIEGHEADDVVATLMEQAV 183
Cdd:cd09860   48 PIVLWDG--RASWRKDLFPEYKANRKKT---REEKKAwreafeaqRPFIEEALEYLGVPQIRAPGAEADDLAGVLVKRLA 122

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 186488278 184 QRGYRAVIASPDKDFKQLISENVqivipladlRRWSFYTLKHYH 227
Cdd:cd09860  123 AFGDKVLLVSGDKDWLQLVYENV---------SWFSPITDKEVT 157

5'-3' exonuclease; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186488278 125 RRELLPSYKAHRKSPNHGRYSKRPhqFVDEVLRKCNVPVVRIEGHEADDVVATLMEQAVQRGYRAVIASPDKDFKQLISE 204
Cdd:PRK14976  70 RHQLYDEYKQGRKKTPESLISQIP--LLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNE 147

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 186488278 205 NVqIVIPLADLRRWSFYTLKHYHAQYNCDPQSDLSFRCIMGDEVDGVPGiqhmVPAFGRKTAMKLVRKHGSLESLL 280
Cdd:PRK14976 148 NT-DVLLKKKGTSHFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKG----VKGIGPKTAIKLLNKYGNIENIY 218

exonuclease

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186488278 125 RRELLPSYKAHRKSpnhgrySKRP---HQFVDEVLRKCNVPVVRIEGHEADDVVATLMEQAVQRGY-RAVIASPDKDFKQ 200
Cdd:PHA00439  78 RKEVVPTYKANRKA------KRKPvgyRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFkKAVLVSCDKDFKT 151

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 186488278 201 lisenvqivIPLADLrrwSFYTLKHYHAQYNCDPQSDLSFRCIMGDEVDGVPGI 254
Cdd:PHA00439 152 ---------IPNCDF---LWCTTGNILTQTPETADRWHLFQTIKGDSTDGYSGI 193

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 186488278 240 FRCIMGDEVDGVPGiqhmVPAFGRKTAMKLVRKHGSLESLLSAAAVRTvgrPYAQEALTKYADYLRRNYQVLAL 313
Cdd:cd09898    7 YLALVGDSSDNIPG----VPGIGPKTAAKLLQEYGSLENILANLDELK---GKLREKLEENKEQALLSRKLATL 73

H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases; 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 Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), 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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 186488278 242 CIM--GDEVDGVPGIqhmvpafGRKTAMKLVRKHGSLESLLSAA 283
Cdd:cd09897    7 CILsgCDYLPGLPGI-------GPKTALKLIKEYGSLEKVLKAL 43

FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Structure-specific 5' nucleases are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner. The family includes the PIN (PilT N terminus) domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the PIN domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4- and T5-5' nucleases, and other homologs. Canonical members of this 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186488278 112 VIAVIDGE-----EGNQRRRELLPSYKAHRKSPN---HGRYSKR--------PHQFVDEVLRKCNVPVVRIEGhEADDVV 175
Cdd:cd09853   46 PILLFDGGkpkakKGNRDKRRERRAREEDRKKGQlkeHKEFDKRlielgpeyLIRLFELLKHFMGIPVMDAPG-EAEDEI 124

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 186488278 176 ATLMEQAVQRGYRAVIASPDKDFKQLISENVQIVIPLADLRRWSF 220
Cdd:cd09853  125 AYLVKKHKHLGTVHLIISTDGDFLLLGTDHPYIPRNLLTVKEETF 169

H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Eukaryotic homologs; Members of this subgroup include the H3TH (helix-3-turn-helix) domains of eukaryotic Flap endonuclease-1 (FEN1), 5' nucleases. 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. 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 subfamily 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. Also, 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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 186488278 242 CIM-G-DEVDGVPGIqhmvpafGRKTAMKLVRKHGSLESLLSA 282
Cdd:cd09907    7 CILlGcDYCESIKGI-------GPKTALKLIKKHKSIEKILEN 42