1CY7,1CY4


Conserved Protein Domain Family
TOPRIM_TopoIA_TopoI

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cd03363: TOPRIM_TopoIA_TopoI 
Click on image for an interactive view with Cn3D
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. 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: 173783
View PSSM: cd03363
Aligned: 39 rows
Threshold Bit Score: 163.501
Threshold Setting Gi: 1351261
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
  • 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:1CY4_A, E.coli Dna Topoisomerase I, bound with thymidine-5'-phosphate, 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-----dYVVKSSVGHIRDLPtsgsaakksadststktakkpkkdergalvnrmgvdpwh 79  Escherichia coli
NP_326302     8 NKLVIVESPNKIKAISKYLGk-----dYVVKASVGHIAYLPasgayglgidle--------------------------- 55  Mycoplasma pulmo...
NP_486671     3 KRLLVVESPGKVKKLSQILGs-----eWIVRASCGHIRELSdegedalgfsmdgs------------------------s 53  Nostoc sp. PCC 7120
AAP84217      1 MHIVIIEAPGKLKKLRSLLPsirpdvtWQVEATAGHIRDLPvhgqdpqmltvgvg------------------------q 56  Pseudomonas aeru...
AAY93915      1 MKLMIIEAPGKLKKLAPMLKklrpgehWEVVASGGHIRDLPekghddtmiiagvl------------------------k 56  Pseudomonas fluo...
BAC88961      2 MRLLICESPGKIKTFKAILGa-----gWDVQASLGHVMELAndgadhlgfdvgpe------------------------a 52  Gloeobacter viol...
ZP_00817865   3 QILVIVESPAKSKKIQTILGs-----nYRVAASVGHMRDLPprdlgvdletl---------------------------- 49  Marinobacter aqu...
YP_424741     2 KVLVLLESPSKIEKIKHYLEesfpeneFVVLASGGHINSIAdkgawglgidle--------------------------- 54  Mycoplasma capri...
AAP58872      3 QTLVIMESPTKTKAVEKYLGe-----nYLVLSSEGHIRNLStkgqyglgvdik--------------------------- 50  Spiroplasma kunk...
ZP_00518345   1 MPLLIVESPNKIKKLRQILGs-----gWLIKASLGHVRELArdgednlgfslnnd------------------------g 51  Crocosphaera wat...
Feature 1                                        # # #                                       
1CY7_A       80 nweahyevlpgkEKVVSELKQLAEkadHIYLATDLDREGEAIAWHLREVIggddaRYSRVVFNEITKNAIRQAFNKP 156 Escherichia coli
NP_326302    56 nwqplmkmdpekRAICKELKEAADkseLVYIATDPDREGESIGQNLVDILkl--kNYKRIVYNEITEQAIKNAINNP 130 Mycoplasma pulmonis...
NP_486671    54 vqchyvprdqrsKETIQQLKSAAKqvsEVVLGTDPDREGETIAWHLKEVLgl--rEPKRVVYTEITASAVQSAIAHP 128 Nostoc sp. PCC 7120
AAP84217     57 dfkphyqilsgkEKTVARLKELRQkavEIYVASDPDREGESIGWHILQAAgi--kNYKRVAFKEITKSCITAELSSP 131 Pseudomonas aeruginosa
AAY93915     57 dlrpvytirdksSGRIKTMREALAratEIYIATDPDREGESIAWHIQQTLri--rDYKRIAFNEVTHTRVKEALANP 131 Pseudomonas fluores...
BAC88961     53 itcryvprgergMATLKKLRTAAAkaqEVYLATDPDREGEAIAWHLARELrl--kSPRRIRCTQITEGAVRTALQSP 127 Gloeobacter violace...
ZP_00817865  50 --kptyvvsegkSQVVSNLKRLAGmsdEVILATDPDREGEAIAWHLKVALrl-pdDVKRVSYQEITRDAIMKAMANP 123 Marinobacter aquaeo...
YP_424741    55 tmqpnfviessrKKIISQIKKEGKtadLIILASDPDREGEAIAYHLANLFkd-htNIKRITFNEITSEAITNAFNNL 130 Mycoplasma capricol...
AAP58872     51 tfepsykmergkKEIIKKLKQEAKaadLIILATDPDREGEAIAYHLNEVLnc-geKSRRVRFNEITKEAVLEAFQHQ 126 Spiroplasma kunkelii
ZP_00518345  52 vscrfvprnskaAKIIKELKTVAKnsnAIYFASDPDREGETIAWHLAQELgv--kNPQRVVYQEITEKAVKAAVKNP 126 Crocosphaera watson...

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