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Conserved domains on  [gi|524856920|emb|CCY25594|]
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primase/helicase [Brachyspira sp. CAG:484]

Protein Classification

Toprim domain-containing protein( domain architecture ID 10484391)

Toprim domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 205-283 4.13e-06

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


:

Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 44.65  E-value: 4.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524856920  205 LAIVEGYMDGYALFQHLQENKQVQYY---HIVTPSNGVNSLLKYINQIEFCKYKKCYLYIDNDEVGKRTAVKILEQYPFM 281
Cdd:pfam01751   2 LIIVEGPSDAIALEKALGGGFQAVVAvlgHLLSLEKGPKKKALKALKELALKAKEVILATDPDREGEAIALKLLELKELL 81


                  ..
gi 524856920  282 KR 283
Cdd:pfam01751  82 EN 83
 
Name Accession Description Interval E-value
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 205-283 4.13e-06

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 44.65  E-value: 4.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524856920  205 LAIVEGYMDGYALFQHLQENKQVQYY---HIVTPSNGVNSLLKYINQIEFCKYKKCYLYIDNDEVGKRTAVKILEQYPFM 281
Cdd:pfam01751   2 LIIVEGPSDAIALEKALGGGFQAVVAvlgHLLSLEKGPKKKALKALKELALKAKEVILATDPDREGEAIALKLLELKELL 81


                  ..
gi 524856920  282 KR 283
Cdd:pfam01751  82 EN 83
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
205-276 4.81e-05

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 41.09  E-value: 4.81e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 524856920   205 LAIVEGYMDGYALFQHLqenkqvQYYHIVTPSNGVNSLLKYINQIEfCKYKKCYLYI--DNDEVGKRTAVKILE 276
Cdd:smart00493   3 LIIVEGPADAIALEKAG------GKRGNVVALGGHLLSKEQIKLLK-KLAKKAEVILatDPDREGEAIAWELAE 69
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 203-276 2.26e-04

Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173773 [Multi-domain]  Cd Length: 83  Bit Score: 39.33  E-value: 2.26e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 524856920 203 NILAIVEGYMDGYALFQHLqenkqvQYYHIVTPSNGVnSLLKYINQIEFCK--YKKCYLYIDNDEVGKRTAVKILE 276
Cdd:cd00188    1 KKLIIVEGPSDALALAQAG------GYGGAVVALGGH-ALNKTRELLKRLLgeAKEVIIATDADREGEAIALRLLE 69
 
Name Accession Description Interval E-value
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 205-283 4.13e-06

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 44.65  E-value: 4.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524856920  205 LAIVEGYMDGYALFQHLQENKQVQYY---HIVTPSNGVNSLLKYINQIEFCKYKKCYLYIDNDEVGKRTAVKILEQYPFM 281
Cdd:pfam01751   2 LIIVEGPSDAIALEKALGGGFQAVVAvlgHLLSLEKGPKKKALKALKELALKAKEVILATDPDREGEAIALKLLELKELL 81


                  ..
gi 524856920  282 KR 283
Cdd:pfam01751  82 EN 83
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 207-295 5.04e-06

Toprim-like; This is a family or Toprim-like proteins.


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 44.09  E-value: 5.04e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524856920  207 IVEGYMDGYALFQHLQENkqvqyYHIVTpSNGVNSLLKYINQIEfcKYKK----CYlyiDNDEVGKRTAVKILEQYP--- 279
Cdd:pfam13155   2 VFEGYIDALSLAQAGIKN-----VLYVA-TLGTALTEAQIKLLK--RYPKevilAF---DNDEAGRKAAKRLAELLKeag 70

                          90
                  ....*....|....*.
gi 524856920  280 FMKRIEMSCGCKDFNE 295
Cdd:pfam13155  71 VDVKIRLLPDGKDWNE 86
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
205-276 4.81e-05

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 41.09  E-value: 4.81e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 524856920   205 LAIVEGYMDGYALFQHLqenkqvQYYHIVTPSNGVNSLLKYINQIEfCKYKKCYLYI--DNDEVGKRTAVKILE 276
Cdd:smart00493   3 LIIVEGPADAIALEKAG------GKRGNVVALGGHLLSKEQIKLLK-KLAKKAEVILatDPDREGEAIAWELAE 69
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 203-278 1.24e-04

Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation.


Pssm-ID: 433387 [Multi-domain]  Cd Length: 85  Bit Score: 39.96  E-value: 1.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524856920  203 NILAIVEGYMDGYALFQHLQENkqvqYYHI----VTPSNGVNSLLKYINQIEfcKYKKCYLYIDNDEVGKRTAVKILEQY 278
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAGYKG----AVAVlggaLSPLDGIGPEDLNIDSLG--GIKEVILALDGDVAGEKTALYLAEAL 74
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 203-276 2.26e-04

Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173773 [Multi-domain]  Cd Length: 83  Bit Score: 39.33  E-value: 2.26e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 524856920 203 NILAIVEGYMDGYALFQHLqenkqvQYYHIVTPSNGVnSLLKYINQIEFCK--YKKCYLYIDNDEVGKRTAVKILE 276
Cdd:cd00188    1 KKLIIVEGPSDALALAQAG------GYGGAVVALGGH-ALNKTRELLKRLLgeAKEVIIATDADREGEAIALRLLE 69
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 203-276 1.23e-03

TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.


Pssm-ID: 173779 [Multi-domain]  Cd Length: 79  Bit Score: 37.25  E-value: 1.23e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 524856920 203 NILAIVEGYMDGYALFQHlqenkqvqYYHIVTPSNGVNSLLKyinQIEFCK--YKKCYLYIDNDEVGKRTAVKILE 276
Cdd:cd01029    1 DEVIIVEGYMDVLALHQA--------GIKNVVAALGTANTEE---QLRLLKrfARTVILAFDNDEAGKKAAARALE 65
TOPRIM_DnaG_primases cd03364
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ...
 207-277 4.08e-03

TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.


Pssm-ID: 173784 [Multi-domain]  Cd Length: 79  Bit Score: 35.57  E-value: 4.08e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 524856920 207 IVEGYMDGYALFQHLQENkqvqyyhiVTPSNGVNS-------LLKYINQIEFCkykkcylyIDNDEVGKRTAVKILEQ 277
Cdd:cd03364    5 LVEGYMDVIALHQAGIKN--------VVASLGTALteeqaelLKRLAKEVILA--------FDGDEAGQKAALRALEL 66
 
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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