Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the archaeal/eukaryal primase (AEP) superfamily. This group includes archaeal plasmids and bacteriophage AEPs. The ORF904 protein is a multifunctional protein having ATPase, primase and DNA polymerase activity, and may play a role in the replication of the archaeal plasmid. The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. For pRN1 primpol, the primase activity prefers dNTPs to rNTPs; incorporation of dNTPs requires rNTP as cofactor. The pRN1 primpol contains an unusual zinc-binding stem, which is not conserved in other members of this group.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844636  18 YAVYPLIENTKKPPKGVVGYQAATSDQNTIFAWFKKHPTYNLGLRLDLSDLLVVDIDMHEPTKNGRTSLAQLFKqgqtLP 97
Cdd:cd04859    1 FAVIPLDPGSKRPLIKGWPKDAATTDPEQIEAWWRDGPDANIGLRTGPSGLVVIDIDVKHDGAAALAALAELGK----LP 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 575844636  98 NDTYIERTANGGVHYFLKYAG---AKVRKIGVWPGIDLLSD--FTVIAPSEINGKQYKPLDSrtLVDIKPAPQWLVDK 170
Cdd:cd04859   77 PLTLTVRTGSGGRHLYFRVPDgvpVKSVKGKGGPGIDIRGGggYVVAPPSVHPGGGYYVWKS--TVDPAPAPEWLLDL 152

Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the archaeal/eukaryal primase (AEP) superfamily. This group includes archaeal plasmids and bacteriophage AEPs. The ORF904 protein is a multifunctional protein having ATPase, primase and DNA polymerase activity, and may play a role in the replication of the archaeal plasmid. The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. For pRN1 primpol, the primase activity prefers dNTPs to rNTPs; incorporation of dNTPs requires rNTP as cofactor. The pRN1 primpol contains an unusual zinc-binding stem, which is not conserved in other members of this group.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844636  18 YAVYPLIENTKKPPKGVVGYQAATSDQNTIFAWFKKHPTYNLGLRLDLSDLLVVDIDMHEPTKNGRTSLAQLFKqgqtLP 97
Cdd:cd04859    1 FAVIPLDPGSKRPLIKGWPKDAATTDPEQIEAWWRDGPDANIGLRTGPSGLVVIDIDVKHDGAAALAALAELGK----LP 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 575844636  98 NDTYIERTANGGVHYFLKYAG---AKVRKIGVWPGIDLLSD--FTVIAPSEINGKQYKPLDSrtLVDIKPAPQWLVDK 170
Cdd:cd04859   77 PLTLTVRTGSGGRHLYFRVPDgvpVKSVKGKGGPGIDIRGGggYVVAPPSVHPGGGYYVWKS--TVDPAPAPEWLLDL 152

Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844636   10 AIELAQQGYAVYPLIENTKKPPkGVVGYQAATSDQNTIFAWFKKHPTYNLGLRLDLSDLLVVDIDMHEptkNGRTSLAQL 89
Cdd:pfam09250   1 ALAYAERGWPVFPLPPGGKHPL-GPGWQKRATTDPEQIRAWWSRHPNANIGLATGPSGLVVLDVDGPE---AGADALARL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844636   90 FKQ-GQTLPnDTYIERTA--NGGVHYFLKYAGAKVRKIG---VWPGIDLLSD--FTVIAPSEINGKQYKPLDSRTlvDIK 161
Cdd:pfam09250  77 EREgGELLP-VTVTVTTGstGGGRHLYFRAPGGLALRNTagkLAGGLDLRGDggYVVAPPSVHTGGAYRWLNGPR--PPA 153

                  ....*
gi 575844636  162 PAPQW 166
Cdd:pfam09250 154 ELPEW 158

Primase C terminal 1 (PriCT-1); This alpha helical domain is found at the C terminal of primases.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 575844636  206 GNRNAWLTKIAGRMFGVGADPKTVYNMLSVINDSFVDPaLPSKEVNVIFQSILKRESK 263
Cdd:pfam08708   8 GGRNNALFRLAGALARRGIDRESVLALLHALNSNLEPP-LDESEVEKTVKSVYRYVYA 64

Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the archaeal/eukaryal primase (AEP) superfamily. This group includes archaeal plasmids and bacteriophage AEPs. The ORF904 protein is a multifunctional protein having ATPase, primase and DNA polymerase activity, and may play a role in the replication of the archaeal plasmid. The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. For pRN1 primpol, the primase activity prefers dNTPs to rNTPs; incorporation of dNTPs requires rNTP as cofactor. The pRN1 primpol contains an unusual zinc-binding stem, which is not conserved in other members of this group.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844636  18 YAVYPLIENTKKPPKGVVGYQAATSDQNTIFAWFKKHPTYNLGLRLDLSDLLVVDIDMHEPTKNGRTSLAQLFKqgqtLP 97
Cdd:cd04859    1 FAVIPLDPGSKRPLIKGWPKDAATTDPEQIEAWWRDGPDANIGLRTGPSGLVVIDIDVKHDGAAALAALAELGK----LP 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 575844636  98 NDTYIERTANGGVHYFLKYAG---AKVRKIGVWPGIDLLSD--FTVIAPSEINGKQYKPLDSrtLVDIKPAPQWLVDK 170
Cdd:cd04859   77 PLTLTVRTGSGGRHLYFRVPDgvpVKSVKGKGGPGIDIRGGggYVVAPPSVHPGGGYYVWKS--TVDPAPAPEWLLDL 152

Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844636   10 AIELAQQGYAVYPLIENTKKPPkGVVGYQAATSDQNTIFAWFKKHPTYNLGLRLDLSDLLVVDIDMHEptkNGRTSLAQL 89
Cdd:pfam09250   1 ALAYAERGWPVFPLPPGGKHPL-GPGWQKRATTDPEQIRAWWSRHPNANIGLATGPSGLVVLDVDGPE---AGADALARL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844636   90 FKQ-GQTLPnDTYIERTA--NGGVHYFLKYAGAKVRKIG---VWPGIDLLSD--FTVIAPSEINGKQYKPLDSRTlvDIK 161
Cdd:pfam09250  77 EREgGELLP-VTVTVTTGstGGGRHLYFRAPGGLALRNTagkLAGGLDLRGDggYVVAPPSVHTGGAYRWLNGPR--PPA 153

                  ....*
gi 575844636  162 PAPQW 166
Cdd:pfam09250 154 ELPEW 158

AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. In addition to its catalytic role in replication, eukaryotic DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. Pfu41 and Pfu46 comprise the primase complex of the archaea Pyrococcus furiosus; these proteins have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41. Also found in this group is the primase-polymerase (primpol) domain of replicases from archaeal plasmids including the ORF904 protein of pRN1 from Sulfolobus islandicus (pRN1 primpol). The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. The pRN1 primpol primase activity prefers dNTPs to rNTPs; however incorporation of dNTPs requires rNTP as cofactor. This group also includes the Pol domain of bacterial LigD proteins such Mycobacterium tuberculosis (Mt)LigD. MtLigD contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. LigD Pol plays a role in non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB) in vivo, perhaps by filling in short 5'-overhangs with ribonucleotides; the filled in termini would be sealed by the associated LigD ligase domain. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 575844636  18 YAVYPLIENTKKPPKGVVGYQAaTSDQNTIFAWFKKHPTYNLGLRL------DLSDLLVVDIDMHEPT--KNGRTSLAQL 89
Cdd:cd00525    1 RPVSPIRPPGKGPFQRHWPFGA-TTDDAEILAWLANLPPGNIGLSLgrydklWKPDLLVFDLDPDDYDcwEDVKEAALLL 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 575844636  90 FKQGQTLPNDTYIERTANGGVHYFLkyagakvrkigvwPGIDLLSD----FTVIAPSEINGK 147
Cdd:cd00525   80 RELLDEDGLNTLVVTSGSRGLHVYV-------------RLIDIRVNargrLLVAPPSVHPRP 128