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Conserved domains on  [gi|543171385|ref|YP_008531665|]
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DNA primase [Propionibacterium phage PHL010M04]

Protein Classification

toprim domain-containing protein( domain architecture ID 10099128)

toprim (topoisomerase-primase) domain-containing protein

Gene Ontology:  GO:0003896

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 146-209 2.10e-07

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: 47.27  E-value: 2.10e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 543171385 146 ICEGEFDSMILEQCG-WPAVAIPGATSWQNFWTKFFEGYDHVYIWSDPDPAGDK-MAQTLQTALPQ 209
Cdd:cd01029    5 IVEGYMDVLALHQAGiKNVVAALGTANTEEQLRLLKRFARTVILAFDNDEAGKKaAARALELLLAL 70
 
Name Accession Description Interval E-value
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 146-209 2.10e-07

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: 47.27  E-value: 2.10e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 543171385 146 ICEGEFDSMILEQCG-WPAVAIPGATSWQNFWTKFFEGYDHVYIWSDPDPAGDK-MAQTLQTALPQ 209
Cdd:cd01029    5 IVEGYMDVLALHQAGiKNVVAALGTANTEEQLRLLKRFARTVILAFDNDEAGKKaAARALELLLAL 70
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 146-207 2.98e-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: 38.42  E-value: 2.98e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171385  146 ICEGEFDSMILEQCGWP-AVAIPGAT-------SWQNFWTKFFEGYDHVYIWSDPDPAGDKMAQTLQTAL 207
Cdd:pfam13662   5 VVEGYADVIALEKAGYKgAVAVLGGAlspldgiGPEDLNIDSLGGIKEVILALDGDVAGEKTALYLAEAL 74
 
Name Accession Description Interval E-value
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 146-209 2.10e-07

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: 47.27  E-value: 2.10e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 543171385 146 ICEGEFDSMILEQCG-WPAVAIPGATSWQNFWTKFFEGYDHVYIWSDPDPAGDK-MAQTLQTALPQ 209
Cdd:cd01029    5 IVEGYMDVLALHQAGiKNVVAALGTANTEEQLRLLKRFARTVILAFDNDEAGKKaAARALELLLAL 70
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 146-198 1.44e-05

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: 42.41  E-value: 1.44e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 543171385 146 ICEGEFDSMILEQCG---WPAVAIPGATSWQNFWT--KFFEGYDHVYIWSDPDPAGDK 198
Cdd:cd00188    5 IVEGPSDALALAQAGgygGAVVALGGHALNKTRELlkRLLGEAKEVIIATDADREGEA 62
TOPRIM_DnaG_primases cd03364
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ...
 146-213 4.33e-05

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: 40.58  E-value: 4.33e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171385 146 ICEGEFDSMILEQCGWP-AVAIPGATSWQNFWTKFFEGYDHVYIWSDPDPAGDKMAQ-TLQTALPQATHV 213
Cdd:cd03364    5 LVEGYMDVIALHQAGIKnVVASLGTALTEEQAELLKRLAKEVILAFDGDEAGQKAALrALELLLKLGLNV 74
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 146-207 2.98e-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: 38.42  E-value: 2.98e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171385  146 ICEGEFDSMILEQCGWP-AVAIPGAT-------SWQNFWTKFFEGYDHVYIWSDPDPAGDKMAQTLQTAL 207
Cdd:pfam13662   5 VVEGYADVIALEKAGYKgAVAVLGGAlspldgiGPEDLNIDSLGGIKEVILALDGDVAGEKTALYLAEAL 74
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 146-211 3.95e-03

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


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 35.62  E-value: 3.95e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171385  146 ICEGEFDSMILEQCG---WPAVAIPGATSWQNFWtKFFEGY-DHVYIWSDPDPAGDKMAQTLQTALPQAT 211
Cdd:pfam13155   2 VFEGYIDALSLAQAGiknVLYVATLGTALTEAQI-KLLKRYpKEVILAFDNDEAGRKAAKRLAELLKEAG 70
 
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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