1GL9


Conserved Protein Domain Family
TOPRIM_TopoIA_RevGyr

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cd03361: TOPRIM_TopoIA_RevGyr 
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TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Statistics
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PSSM-Id: 173781
View PSSM: cd03361
Aligned: 14 rows
Threshold Bit Score: 249.153
Threshold Setting Gi: 18312412
Created: 27-Dec-2005
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 6 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:By similarity to E. coli DNA topoisomerase I and III.
  • Comment:involved in both strand cleavage and rejoining
  • Comment:reaction is Mg2+ dependent
  • Citation:PMID 9722641

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1            ##  #                                                                     
1GL9_B     506 PALFIVESPTKARQISRFFGKPSVKVLDGAVVYEIPMQk------yVLMVTASIGHVVDLITnrgfhg------------ 567  Archaeoglobus fu...
AAR39166    41 MVLFIVESPNKARTIANFFGKPSVRRIGNIKAYETTTGk------yILTIVATKGHLFELTLkeegvy------------ 102  Nanoarchaeum equ...
NP_559079  635 TILMVVESPTKARTIANFFGRPSLIISEGIPIYEVSTGd------aVLMVTASLGHIYELPTslnkidqrqrevlakwfg 708  Pyrobaculum aero...
NP_623335  555 SRMIIVESPTKAQTISKFLEKSSTRRYGSLMVHESITQe------gILLLTASKGHLYDLETktglhg------------ 616  Thermoanaerobact...
NP_227988  542 SLLIIVESPTKAETLSRFLGRASSRKERNIIVHEAVTGe------gVILFTATRGHVYDLVTkggihg------------ 603  Thermotoga marit...
BAD71968   555 ERVVVVESPNKARTLAGFFGRPMRRYLPGLVVYEALSEe------gYLVVTATRGHVTDLALrgglyg------------ 616  Thermus thermoph...
NP_342447  580 TGLLIVESPTKAKTIAKMFSRPSVRIRNKVPVYETIIVdgn--qiyVLDIVASKGHIVDLTLedigyyg----------- 646  Sulfolobus solfa...
AAK40747   619 TTLFIVESPNKAKTISNFFSRPSTRSYGKLRVYETVLGd------rVLIVAASGGHIYDLITedesekqddn-------- 684  Sulfolobus solfa...
BAA80373   625 TTLLVVESPTKARTIAWFWGRPGKRRIGRSVIYEASVSdpetgdvhILQITSTRGHLTDLTTdsvgsky----------- 693  Aeropyrum pernix K1
BAA29893   640 SALMIVESPNKARTIASFFGQPSKRKIGDLTAYEVSIGd------kMLTILASGGHMFDLVTnegyhgvl---------- 703  Pyrococcus horik...
Feature 1                                                                                     #
1GL9_B     568 --------------vlvngRFVPVYASIKRCRDCgyqft--edresCPKCgsenvdnsRSRIEALRKLAHdaeFVIVGTD 631  Archaeoglobus fu...
AAR39166   103 -------------gvlkekEYVPIFSPIKKCLDCghqfv---dedkCPRCgseniddaSDRIKVLRDLAQeadIVLIGTD 166  Nanoarchaeum equ...
NP_559079  709 dfkhgnydgenyavivkeyGFVPVYNKIWRCRGAvyvd----didiPPGCk------pLDVLEAIRNIAVevdTVLLGTD 778  Pyrobaculum aero...
NP_623335  617 -------------veindgRFIPYYNSIKRCSSCgaqft--delprCPYCnsdkiddkKKILEALRDIAMevdEVIIATD 681  Thermoanaerobact...
NP_227988  604 -------------veeengKFVPVYNSLKRCRDCgyqft--edrdeCPVCsskniddkTETLRALREISLeadEILVATD 668  Thermotoga marit...
BAD71968   617 --------------vetapAYRPRYHPLRACPEGsvp------dpfCPDGrasr-pdrDRALEALRSLALeaqDFLLATD 675  Thermus thermoph...
NP_342447  647 ------------ikveddgTIKPYYDLIKKCLDCnkifs--sasdkCPYCgsanlqsaQTTINLLRELALsvdKVFIASD 712  Sulfolobus solfa...
AAK40747   685 ---------yvygvlvkdsKFIPIYSTIKKCEKGhqivkd-lsqnkCPICgsrivtdkTEVVDILRKLALevdEVLIGTD 754  Sulfolobus solfa...
BAA80373   694 ------------gvdedggGYRAYYSTIKRCLDCgaqht--ssspfCPRCgsprqvdsKSVVEILRKLASevdEIVIATD 759  Aeropyrum pernix K1
BAA29893   704 -----------ilknngkpYFVPVYDTIKRCRDCghqfvdweqkgvCPRCgsrnvhdaLENVKAMRELALevdEILIGTD 772  Pyrococcus horik...
Feature 1       # #                                       
1GL9_B     632 PDTEGEKIAWDLKNLlsg-cgAVKRAEFHEVTRRAILEALESL 673  Archaeoglobus fulgidus
AAR39166   167 PDAEGEKIAYDVYSIirpynkNIYRAEFHEVTRQAIIKALEEI 209  Nanoarchaeum equitans Kin4-M
NP_559079  779 PDSEGEKIAFDLYLGlrpyvqDIRRVEFHEVTRRAILNALANP 821  Pyrobaculum aerophilum str. IM2
NP_623335  682 PDVEGEKIGWDISQYikpvnkNVQRIEMHEITKFGFDKAIRNR 724  Thermoanaerobacter tengcongensis MB4
NP_227988  669 PDVEGEKISWDVTQYllpstrSLRRIEMHEITRYGFKKARESV 711  Thermotoga maritima MSB8
BAD71968   676 PDTEGEKIAWDVLLAlrafgkEVARGEFHAVTPRAFLEALRRP 718  Thermus thermophilus HB8
NP_342447  713 PDTEGEKIAYDLASFlspynsNVYRVVYHEITKKAILEALRNP 755  Sulfolobus solfataricus P2
AAK40747   755 PDTEGEKIAWDIYLAirpfngNIKRAEFHEVTRRAILNAIKNP 797  Sulfolobus solfataricus P2
BAA80373   760 PDREGEKIAWDVFLAvrpynpNVRRGRFHEVTPRAVIEALRSG 802  Aeropyrum pernix K1
BAA29893   773 PDTEGEKIAWDIRNVlapyapNIKRIEFHEVTRPAILRAIREA 815  Pyrococcus horikoshii OT3

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