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Conserved domains on  [gi|446563520|ref|WP_000640866|]
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MULTISPECIES: toprim domain-containing protein [Bacillus]

Protein Classification

toprim domain-containing protein( domain architecture ID 10004131)

toprim (topoisomerase-primase) domain-containing protein similar to Bacillus subtilis protein YusF

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 4-82 1.55e-15

TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). 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.


:

Pssm-ID: 173777  Cd Length: 81  Bit Score: 65.74  E-value: 1.55e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446563520   4 VEKVIIVEGKSDRRKIESIIREpVEIVCTNGTIGLSKMDELIDQFfDKEVYVLVDADDAGEKLRKQFRKEF----PQAEH 79
Cdd:cd01027    1 IGEVIIVEGKNDTESLKKLGIE-AEIIETNGSIINKETIELIKKA-YRGVIILTDPDRKGEKIRKKLSEYLsgpvPEIKR 78


                 ...
gi 446563520  80 IYI 82
Cdd:cd01027   79 AFL 81
 
Name Accession Description Interval E-value
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 4-82 1.55e-15

TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). 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.


Pssm-ID: 173777  Cd Length: 81  Bit Score: 65.74  E-value: 1.55e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446563520   4 VEKVIIVEGKSDRRKIESIIREpVEIVCTNGTIGLSKMDELIDQFfDKEVYVLVDADDAGEKLRKQFRKEF----PQAEH 79
Cdd:cd01027    1 IGEVIIVEGKNDTESLKKLGIE-AEIIETNGSIINKETIELIKKA-YRGVIILTDPDRKGEKIRKKLSEYLsgpvPEIKR 78


                 ...
gi 446563520  80 IYI 82
Cdd:cd01027   79 AFL 81
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 7-84 9.08e-13

5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 61.20  E-value: 9.08e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446563520   7 VIIVEGKSDRRKIESIIRepVEIVCTNGTIGLSKMDELIDQFFDK-EVYVLVDADDAGEKLRKQFRKEFPQAEHIYIDR 84
Cdd:COG1658   10 VIVVEGKDDTAALKRAVD--ADIIETNGSAISEETLELIKVAAEKrGVIILTDPDRAGERIRKRISEHLPGAKHAFIDR 86
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
5-77 5.07e-08

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 46.49  E-value: 5.07e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446563520     5 EKVIIVEGKSDRRKIESIIREPVEIVCTNGTIGLSKMDELIDQFFDK-EVYVLVDADDAGEKLRKQFRKEFPQA 77
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLLSKEQIKLLKKLAKKaEVILATDPDREGEAIAWELAELLKPA 74
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 6-79 4.12e-05

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: 39.26  E-value: 4.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446563520    6 KVIIVEGKSDRRKIESII-REPVEIVCTNGTI------GLSKMDELIDQFF--DKEVYVLVDADDAGEKLRKQFRKEFPQ 76
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALgGGFQAVVAVLGHLlslekgPKKKALKALKELAlkAKEVILATDPDREGEAIALKLLELKEL 80


                  ...
gi 446563520   77 AEH 79
Cdd:pfam01751  81 LEN 83
 
Name Accession Description Interval E-value
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 4-82 1.55e-15

TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). 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.


Pssm-ID: 173777  Cd Length: 81  Bit Score: 65.74  E-value: 1.55e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446563520   4 VEKVIIVEGKSDRRKIESIIREpVEIVCTNGTIGLSKMDELIDQFfDKEVYVLVDADDAGEKLRKQFRKEF----PQAEH 79
Cdd:cd01027    1 IGEVIIVEGKNDTESLKKLGIE-AEIIETNGSIINKETIELIKKA-YRGVIILTDPDRKGEKIRKKLSEYLsgpvPEIKR 78


                 ...
gi 446563520  80 IYI 82
Cdd:cd01027   79 AFL 81
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 7-84 9.08e-13

5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 61.20  E-value: 9.08e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446563520   7 VIIVEGKSDRRKIESIIRepVEIVCTNGTIGLSKMDELIDQFFDK-EVYVLVDADDAGEKLRKQFRKEFPQAEHIYIDR 84
Cdd:COG1658   10 VIVVEGKDDTAALKRAVD--ADIIETNGSAISEETLELIKVAAEKrGVIILTDPDRAGERIRKRISEHLPGAKHAFIDR 86
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
5-77 5.07e-08

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 46.49  E-value: 5.07e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446563520     5 EKVIIVEGKSDRRKIESIIREPVEIVCTNGTIGLSKMDELIDQFFDK-EVYVLVDADDAGEKLRKQFRKEFPQA 77
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLLSKEQIKLLKKLAKKaEVILATDPDREGEAIAWELAELLKPA 74
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 6-68 4.59e-07

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: 43.95  E-value: 4.59e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446563520   6 KVIIVEGKSDRRKIESIIREPVEIVCTNGTIGLSKMDELIDQF-FDKEVYVLVDADDAGEKLRK 68
Cdd:cd00188    2 KLIIVEGPSDALALAQAGGYGGAVVALGGHALNKTRELLKRLLgEAKEVIIATDADREGEAIAL 65
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 6-79 4.12e-05

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: 39.26  E-value: 4.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446563520    6 KVIIVEGKSDRRKIESII-REPVEIVCTNGTI------GLSKMDELIDQFF--DKEVYVLVDADDAGEKLRKQFRKEFPQ 76
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALgGGFQAVVAVLGHLlslekgPKKKALKALKELAlkAKEVILATDPDREGEAIALKLLELKEL 80


                  ...
gi 446563520   77 AEH 79
Cdd:pfam01751  81 LEN 83
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-65 8.21e-05

Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains [Replication, recombination and repair];


Pssm-ID: 442812 [Multi-domain]  Cd Length: 359  Bit Score: 39.99  E-value: 8.21e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446563520   1 MIYVEKVIIVEGKSD--------RRKIESIIREPVEIVCTNGTIGLSKMDELIdQFFDKEVYVLVDADDAGEK 65
Cdd:COG3593  277 LLFARKVILVEGDTEvillpalaRKLGKDLDEEGISIIPVGGKSNLKPLAKLL-KALGIPVAVLTDGDEAGKA 348
OLD-like_TOPRIM pfam20469
Overcoming lysogenization defect protein-like, TOPRIM domain; This entry represents the ...
 5-60 8.56e-03

Overcoming lysogenization defect protein-like, TOPRIM domain; This entry represents the topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain. The nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. The TOPRIM domain has two conserved motifs, one of which centres at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 466618  Cd Length: 67  Bit Score: 32.36  E-value: 8.56e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446563520    5 EKVIIVEGKSDRRKIESIIREP---------VEIVCTNGTIGLSKMDELIdQFFDKEVYVLVDAD 60
Cdd:pfam20469   4 DKVILVEGDTEEILLPALAEKLlgkdldalgISIVSVGGKGNFKRFLKLL-KALGIPVAVITDLD 67
 
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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