1CY7,1DD9,1I7D,1DDE,1CY4,1GL9,1VDD,2AU3,1BGW,1D3Y,1T6T


Conserved Protein Domain Family
TOPRIM

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cd00188: TOPRIM 
Click on image for an interactive view with Cn3D
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.
Statistics
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PSSM-Id: 173773
View PSSM: cd00188
Aligned: 610 rows
Threshold Bit Score: 30.0876
Threshold Setting Gi: 71850865
Created: 1-Nov-2000
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
active sitemetal binding
Conserved site includes 6 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:involved in both strand cleavage and rejoining
  • Comment:reaction is Mg2+ dependent
  • Comment:catalytic mechanism of ssDNA cleavage in 1I7D_A: active site tyrosine forms a covalent linkage with the 5' phosphate of the scissile bond and conserved glutamate of TOPRIM domain donates a proton to the leaving 3' oxygen of the scissile bond
  • Structure:1I7D_A; Escherichia coli topoisomerase III with bound ssDNA, contacts at 3.5A
    View structure with Cn3D
  • Citation:PMID 9722641

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1             ##  #                                                                     
1CY7_A        5 KALVIVESPAKAKTINKYlgs-------------dyvVKSSVGhirdlptsgsaakksadststktakkpkkdergalvn 71  Escherichia coli
1I7D_A        1 MRLFIAEKPSLARAIADVlpkphrkgdgfiecgngqvVTWCIGhlleqaqpdaydsryarwnlad--------------- 65  Escherichia coli
AAS11862    257 KSVILCEGYMDVLAFFQAgi---------------enAVAPLGtal---------------------------------- 287 Treponema dentic...
O83505      257 RAAIICEGYMDVIAFHQAql---------------tyAVAPLGall---------------------------------- 287 Treponema pallidum
NP_662471   254 ETAILVEGYMDVIAMHQAgf---------------tnTVASCGtal---------------------------------- 284 Chlorobium tepid...
BAD39572    257 NQAILVEGYMDVLMPHQAgi---------------qnVVAPLGtal---------------------------------- 287 Symbiobacterium ...
ZP_00665230 261 RQTVLVEGYMDLLAFHARgf---------------frVVATLGtal---------------------------------- 291 Syntrophobacter ...
CAI82715    252 NRAIIVEGYMDAIMSHQGgf---------------tyTVACMGtal---------------------------------- 282 Dehalococcoides ...
BAB73280    265 DQAVVVEGYFDAIALHAAgi---------------nhAVASLGtal---------------------------------- 295 Nostoc sp. PCC 7120
P74143      265 DEAILVEGYFDVIALHESgi---------------kqTVAALGial---------------------------------- 295 Synechocystis sp...
Feature 1                                                  # # #                            
1CY7_A       72 rmgvdpwhnweahyevlpgkekvvsELKQLAek--adHIYLATDLDREgeaiAWHLREViggd----darYSRVVF 141 Escherichia coli
1I7D_A       66 ----lpivpekwqlqprpsvtkqlnVIKRFLhe--asEIVHAGDPDREgqllVDEVLDYlqlap-ekrqqVQRCLI 134 Escherichia coli
AAS11862    288 ----------------------tedQVKLLKsf--aeTFYLAFDSDKAgqeaSYKAIKIcrsm----gvnVRVLYI 335 Treponema denticola ...
O83505      288 ----------------------tksQARLMRsf--vdRIYMCFDADGAgraaTYKAILLcrsl----gfeVRIVEL 335 Treponema pallidum
NP_662471   285 ----------------------tryQAKILKry--tsRVLFLYDGDNAgkksMLAGIDIllse----gltPWVVML 332 Chlorobium tepidum TLS
BAD39572    288 ----------------------tdeQVRIIRqq--aqQVIVAFDMDTAgqlaTLRGLQKlyds----gcdVRVLQL 335 Symbiobacterium ther...
ZP_00665230 292 ----------------------tphQVRILSrm--sdEVVMAYDGDEAgdkaMLRGLPLflqe----nvaVSCVRF 339 Syntrophobacter fuma...
CAI82715    283 ----------------------terQIALIKrq--tkNLVLGLDSDSAgeeaTLRAIDYenqm----eseIRVAVP 330 Dehalococcoides sp. ...
BAB73280    296 ----------------------sleQVRLILrytdskQLVLNFDADKAgtnaAERAIGEiadlaykgevqLKILNI 349 Nostoc sp. PCC 7120
P74143      296 ----------------------srdQVQSLMrfsqskQIIFNFDADKAginaTQRAIQEieplvysgqvnLRILNL 349 Synechocystis sp. PC...

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