Conserved Protein Domain Family
TOPRIM_TopoIIA_GyrB

?
cd03366: TOPRIM_TopoIIA_GyrB 
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. 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 strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Statistics
?
PSSM-Id: 173786
View PSSM: cd03366
Aligned: 26 rows
Threshold Bit Score: 222.916
Threshold Setting Gi: 1107468
Created: 28-Dec-2005
Updated: 2-Oct-2020
Structure
?
Aligned Rows:
 
active siteputative
Feature 1:active site [active site]
Evidence:
  • Comment:by similarity to other TOPRIM containing proteins such as DnaG primase.
  • Comment:involved in both strand cleavage and rejoining
  • Comment:reaction is Mg2+ dependent
  • Citation:PMID 9722641
  • Citation:PMID 8538787

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
Feature 1           ##  #                                                                     
EAM55518  433 CELFLVEGESAGGTAKQGRERrFQAILPLKGKILNVEKarydKMLGHEEIRCMITALGtgigkddfDVAKLRYDKIIIMT 512 Solibacter usitatu...
AAB67237  416 REIYIVEGDSAGGSAKMGRNRfFQAILPLWGKMLNVEKtredKVITNDKLIPIIASLGagvg-ktfDITKLRYHKIIIMA 494 Lyme disease spiro...
AAC07098  423 CEIFLVEGDSAGGSAKQARDRrYQAILPLRGKIINVEKaridKVLSNDEIKAIVSALGcgig-edlDLKKLRYHKIILMT 501 Aquifex aeolicus VF5
AAD35915  421 TELFIVEGDSAGGSAKQARDReFQAVLPIRGKILNVEKssldRLLKNEQISDIIVAVGtgig-ddfDESKLRYGRIIIMT 499 Thermotoga maritim...
O29720    419 RELFIVEGESAGGSAKQARDRrFQAILPIKGKIINVEKagmaRVLKNDEIKAIISAIGagig-kdfDITKARYRRIIIMT 497 Archaeoglobus fulg...
NP_207298 416 SEIFLVEGDSAGGSAKQGRDRvFQAILPLKGKILNVEKshlsKILKSEEIKNMITAFGcgiq-esfDIERLRYHKIIIMT 494 Helicobacter pylor...
NP_279848 395 AELFVVEGDSAGGSAKQGRNPgFQAILPLGGKILNVEKhrldRILEHDELRHIITALGtgig-defDIDELRYENIIMMT 473 Halobacterium sp. ...
AAM73478  426 CELYIVEGDSAGGSAKQGRDRsFQAILPLKGKILNVEKarlhKMLENEEIKTIILALGtsigeeefSPEKLRYGKIIIMT 505 Chlorobium tepidum...
CAD76089  500 CEVYLVEGDSAGGSAEGGRMReYQAILPLRGKIINAYKsredKVLANEEVQSMIQAIGtgig-adqDLSRRRYNKVIIMT 578 Rhodopirellula bal...
AAP98215  431 CEMYIVEGDSAGGSAKQGRDRrFQAILPIRGKILNVEKarlqKIFQNQEIGTIIAALGcgigadnfNLSKLRYRRIIIMT 510 Chlamydophila pneu...
Feature 1     # # #                              
EAM55518  513 DADVDGSHIRTLLLTFFFRhMNELITrGKVYIAQP 547 Solibacter usitatus Ellin6076
AAB67237  495 DADVDGSHIRTLLLAFFFRyMRDLIEnGYIYIAMP 529 Lyme disease spirochete
AAC07098  502 DADVDGSHIRTLLLTFFYRfMPKLVEeGYVYIAEP 536 Aquifex aeolicus VF5
AAD35915  500 DADIDGAHIRTLLLTLFYRyMRPLIEqGRVYIALP 534 Thermotoga maritima MSB8
O29720    498 DADVDGAHIRTLLLTFFYRyMRPLIEsGYLYIAQP 532 Archaeoglobus fulgidus
NP_207298 495 DADVDGSHIQTLLMTFFYRyLRPLIEqGHVYIAQA 529 Helicobacter pylori 26695
NP_279848 474 DADVDGAHIRTLLLTFFYRhMKPLLEaGYVYAAQP 508 Halobacterium sp. NRC-1
AAM73478  506 DADVDGAHIRTLLLTFFFRyMRSLIEaGKVFIAQP 540 Chlorobium tepidum TLS
CAD76089  579 DADVDGSHIRTLLLCFFYRqMYQLVAaGHVYVAQP 613 Rhodopirellula baltica SH 1
AAP98215  511 DADVDGSHIRTLLLTFFYRhMTALIEnECVYIAQP 545 Chlamydophila pneumoniae TW-183

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap