1BGW


Conserved Protein Domain Family
TOPRIM_TopoIIA

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cd03365: TOPRIM_TopoIIA 
Click on image for an interactive view with Cn3D
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. 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. 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 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
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PSSM-Id: 173785
View PSSM: cd03365
Aligned: 22 rows
Threshold Bit Score: 211.775
Threshold Setting Gi: 27447212
Created: 28-Dec-2005
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
active siteputative
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 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
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Format: Row Display: Color Bits: Type Selection:
Feature 1            ##  #                                                                     
1BGW        35 CTLVLTEGDSALSLAVAGLA--VVGRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLqhrk---kyeDTKSLR 109  baker's yeast
1174740    455 CTLILTEGDSAKSLALAGRS--VLGNNYCGVFPLRGKLLNVREASTTQITNNKEIENLKKILGLkqnm---kyeNVNSLR 529  thale cress
6094499    559 CTLIITEGDSAKSLALAGLS--VVGRNSYGVFPLRGKLLNVRDVASKQLLSNEEINNLTTILGLshknsydtdeSMEDLR 636  Dictyostelium di...
AAL99217   445 RTLIVTEGDSAKALALNSLS--NEQRKYFGVFPLRGKLLNVRNNNLARLKKCKELCDLFAALGIeigr---rytSTESLR 519  Bodo saltans
AAP33503   507 CTLILTEGDSAKALAVDGISsiEDGKKYYGVFPLRGKVINVRNESIDKVSNNAEITNLKKILGLkqgmdystqeARNTLR 586  Giardia intestin...
XP_326193  562 CTLILTEGDSARGLAVAGRA--ILDPNRIGVFPLRGKMLNVRDASADQILKNKEVENIKKFLGLkhgk---vytDTKDLR 636  Neurospora crassa
AAR91745   427 CTLILTEGDSAKTLAVSGLS--VVGRDYYGVFPLRGKPLNAREIAPSKVKENHEFENIAKIMGLrygk---vytSIDELR 501  Entamoeba histol...
AAH72193   453 CTLILTEGDSAKTLAVSGLG--VVGRDRYGVFPLRGKLLNVREASHKQIMENAEINNIIKIVGLqykknyddneSLRTLR 530  African clawed frog
AAT68150   454 CTLILTEGDSAKTLAVSGLG--VVGRDRYGVFPLRGKMLNVREASHKQIMENAEINNIIKILGLqykknysdpeSLKSLR 531  zebrafish
XP_783546  480 CTLILTEGDSAKSLAVSGLG--VVGRDHYGVFPLRGKLLNVREASHKQIMENAEINNIIKILGLqyknkydspeSLKSLR 557  purple urchin
Feature 1              # # #                                
1BGW       110 YGHLMIMTDQDHDGSHIKGLIINFLEssFLGLLDi-qGFLLEFIT 153  baker's yeast
1174740    530 YGQMMIMTDQDHDGSHIKGLLINFIHsfWPSLLQv-pSFLVEFIT 573  thale cress
6094499    637 YGRVMIMADQDHDGSHIKGLVMNFIHyfWPNLLKr--GFLVEFVT 679  Dictyostelium discoideum
AAL99217   520 YQRLLVMTDQDADGTHIKGLLISAFEslWPSLLQhslGFISIFST 564  Bodo saltans
AAP33503   587 YGHVMIMTDQDPDGSHIKGLLINLFDtyWNGLARs-nKFLDFFIT 630  Giardia intestinalis
XP_326193  637 YGHLMIMADQDLDGSHIKGLLINFFEcqFPSLLRi-pNFFQEFIT 680  Neurospora crassa
AAR91745   502 YGSVMIMADQDFDGSHIKGLLINYFHtfWPSLLKi-dNFLVEFIT 545  Entamoeba histolytica
AAH72193   531 YGKIMIMTDQDQDGSHIKGLLINFIHhnWPSLLKh--CFLEEFIT 573  African clawed frog
AAT68150   532 YGKLMIMTDQDQDGSHIKGLLINFIHhnWPSLLRh--NFLEEFIT 574  zebrafish
XP_783546  558 YGRLMIMTDQDQDGSHIKGLLINFIHsnWPHLLQr--NFLEEFIT 600  purple urchin

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