1I7D


Conserved Protein Domain Family
TOPRIM_TopoIA_TopoIII

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cd03362: TOPRIM_TopoIA_TopoIII 
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TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. 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. 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: 173782
View PSSM: cd03362
Aligned: 77 rows
Threshold Bit Score: 114.638
Threshold Setting Gi: 71076169
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:involved in both strand cleavage and rejoining
  • Comment:reaction is Mg2+ dependent
  • Structure:1I7D_A; Escherichia coli topoisomerase III with bound ssDNA, contacts at 3.5A
    View structure with Cn3D
  • 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
  • Citation:PMID 9722641

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1             ##  #                                                                     
1I7D_A        1 MRLFIAEKPSLARAIADVLPkphrkgdg------------fiecgngQVVTWCIGHLLEQAqpdaydsryarwnladlpi 68   Escherichia coli
NP_560414     1 MKLIVAEKRSVAQSIAKFLGrsyksqklygv-----svyrfnygggeAVAIGLSGHIMDFDfaarqnvwtwlppee---l 72   Pyrobaculum aer...
NP_617416     1 MHLIVTEKNIAARRIAAILApkspkkervsgvdvyryelgkgksrqeTAVVGLSGHIVGIDfqkeynnwqkvdar----- 75   Methanosarcina ...
O28469        4 SWLIITEKDNTARRIASILFkdvktlkkgr-------vsyyhspsndAYVVGLKGHIVELDfpkelnnwtktple----- 71   Archaeoglobus f...
Q9HM08        4 FRIIIAEKADAGRRIAYFLSggqvkshrakgt----sylefeyngskTYLIPLSGHIVEADfesgysdwnkidls----- 74   Thermoplasma ac...
NP_444190     1 MELIVTEKNNAARRIADILSeggasttqta--------gvnvyewggRRCIGLSGHVVGVDfppeyndwrdvepa----- 67   Halobacterium s...
AAM05195      2 TVVAFAEKNKAAAQIASILGdgevdkisvegl----payefkwkgeeWLVMGLSGHIMNYDfpeqynkwsevnpg----- 72   Methanosarcina ...
ZP_00869315   1 MHLIIAEKNIAANRIAQILSgkdkvsakke-------ggvnvytfgdKISIGLRGHVVEVDfvegytnwrsqerpp---r 70   Methanospirillu...
ZP_00601990   1 MRLIISEKANAARKIAQFLAegpvkegkhrsv----pyhtftwrgeeCVSVGLKGHVLNPEypeeysnwqkvdpr----- 71   Rubrobacter xyl...
AAB86097      9 HEVIICEKPKSSEKIAGALFpdamkkkhgkv-----sywehvegdkrVTIVSAVGHLYSLRprqsneehffdlew----- 78   Methanothermoba...
Feature 1                                         # # #                                         
1I7D_A       69 vpekwqlqprpsvTKQLNVIKRFLHeasEIVHAGDPDREGQLLVDEVLDYlqlap-ekrqQVQRCLINDLNPQAVERAID 147  Escherichia coli
NP_560414    73 fnatpilvlrgetLKYVKALKSLATkadEVYLALDADVEGEAIAYETALVvkmv--npraRLYRVRFNAVTYKEIVSAFQ 150  Pyrobaculum aer...
NP_617416    76 alidaeitttpinRKIVTALRTLGKeadRVTIATDYDREGELIGVEALNIikkv--npevPFDRVRYSAITPKAIDAAFT 153  Methanosarcina ...
O28469       72 kllqaelvkkvkeRTISSILKEIAKkadRVTVATDYDREGELIGVEALEIvksv--nptvKVDRVRYSAVTEKEIRSAFS 149  Archaeoglobus f...
Q9HM08       75 dlidarivkniknKVAYQTLQAFRGkveEIVIATDYDREGELIGVEALDIike----gkeEIRRAKFSALTKNEILDSFK 150  Thermoplasma ac...
NP_444190    68 elihadvvkdptqEDIVNALQRLAReadDVVIATDYDREGELIGKEAYELvrev--neqaPVNRVRFSSITDTEVRSAFA 145  Halobacterium s...
AAM05195     73 tllgvdpekfvtrAEYATAIKKLAKradKIILACDYDREGENIGFEAKTLaeev---tdvPVARARFSALSPKEVRKAFE 149  Methanosarcina ...
ZP_00869315  71 slidaetikrptePAIVKLIHKIAKkanRVTIATDFDTEGELIGKEAYELvrav--npkvPIDRARFSAITKEEINRAFS 148  Methanospirillu...
ZP_00601990  72 elidarilksvseKGVAAAVRSLAKkadRVIIATDFDREGELIGVEALSLafeanpalmdHVERARFSALTKGEVTRAFE 151  Rubrobacter xyl...
AAB86097     79 apiheidkkkgyvKDYLNVIRKFAAgadRYIHACDYDIEGTLIGFNALKYgcge--ealrKTSRMKFSTLTREEIQRAYK 156  Methanothermoba...
Feature 1         
1I7D_A      148 RL 149  Escherichia coli
NP_560414   151 KP 152  Pyrobaculum aerophilum str. IM2
NP_617416   154 NP 155  Methanosarcina acetivorans C2A
O28469      150 KP 151  Archaeoglobus fulgidus
Q9HM08      151 NL 152  Thermoplasma acidophilum
NP_444190   146 DP 147  Halobacterium sp. NRC-1
AAM05195    150 SP 151  Methanosarcina acetivorans C2A
ZP_00869315 149 EP 150  Methanospirillum hungatei JF-1
ZP_00601990 152 NL 153  Rubrobacter xylanophilus DSM 9941
AAB86097    157 NP 158  Methanothermobacter thermautotrophicus str. Delta H

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