1CY7,1I7D,1GL9,1CY4


Conserved Protein Domain Family
TOPRIM_TopoIA

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cd01028: TOPRIM_TopoIA 
Click on image for an interactive view with Cn3D
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow 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: 173778
View PSSM: cd01028
Aligned: 137 rows
Threshold Bit Score: 66.095
Threshold Setting Gi: 78033849
Created: 1-Nov-2000
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
  • 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-------------dYVVKSSVGHIRDLPtsgsaakksadststktakkpkkdergalvn 71   Escherichia coli
1I7D_A         1 MRLFIAEKPSLARAIADVLPkphrkgdgfiecgngQVVTWCIGHLLEQAqpdaydsryarwnlad--------------- 65   Escherichia coli
1CY4_A         5 KALVIVESPAKAKTINKYLGs-------------dYVVKSSVGHIRDLPtsgsaakksadststktakkpkkdergalvn 71   Escherichia coli
NP_295097     46 KTLVIVESPAKAKTIEKYLGq-------------gYAVESSVGHIRDLPrsaadipekykgqawarl------------- 99   Deinococcus ra...
P39814         3 DYLVIVESPAKAKTIERYLGk-------------kYKVKASMGHVRDLPksqmgvdieqn-------------------- 49   Bacillus subtilis
CAD75669      31 KSLVIVESPAKARTISKFLGs-------------gYQVEASVGHVRDLPggakdipkkfkkepwayl------------- 84   Rhodopirellula...
AAQ65921       2 KNLVIVESPAKAKTIGRFLGs-------------dYTVLSSYGHIRDLKpnkfsvdiqnn-------------------- 48   Porphyromonas ...
EAM54240       3 KALVIVESPAKAKTINKYLGk-------------qYVVKASLGHIKDLPkrdlavdvehg-------------------- 49   Solibacter usi...
ZP_00769790   18 RRLVIVESPTKARKLASYLGs-------------gYIVESSRGHIRDLPraasdvpakyksqpwarl------------- 71   Mycobacterium ...
BAB81408       3 QKLVIVESPAKAKTIEKYLGk-------------nYVVEASMGHVRDLPksqlgvdiene-------------------- 49   Clostridium pe...
Feature 1                                                 # # #                                  
1CY7_A        72 rmgvdpwhnweahyevlpgkEKVVSELKQLAEkadHIYLATDLDREGEAIAWHLREVigg---ddaRYSRVVFNEITKNA 148  Escherichia coli
1I7D_A        66 ----lpivpekwqlqprpsvTKQLNVIKRFLHeasEIVHAGDPDREGQLLVDEVLDYlqlapekrqQVQRCLINDLNPQA 141  Escherichia coli
1CY4_A        72 rmgvdpwhnweahyevlpgkEKVVSELKQLAEkadHIYLATDLDREGEAIAWHLREVigg---ddaRYSRVVFNEITKNA 148  Escherichia coli
NP_295097    100 --gldvehdfqplyvvspekKQKVAQLRKLAAeadEIILATDDDREGESIAWHLYQElkp----kvPVKRMVFHEITREA 173  Deinococcus ra...
P39814        50 ---------fepkyitirgkGPVLKELKTAAKkakKVYLAADPDREGEAIAWHLAHSldl---dlnSDCRVVFNEITKDA 117  Bacillus subtilis
CAD75669      85 --gvnvekdfepvyivpadkKKQVDKLKAALKdadSLYLATDEDREGEAISWHLFELlkp----kvPVHRLVFHEITKEA 158  Rhodopirellula...
AAQ65921      49 ---------yepeyeipadkRPVVKELKSQADrsdFIWLASDEDREGEAIAWHLYEAlgl---knkQTKRIVFHEITETA 116  Porphyromonas ...
EAM54240      50 ---------fepryeiiegkKKLMGELRSAAKgvdQIYLAADPDREGEAICFHLQEElrsk-kdgpAFFRVMFNEITKKA 119  Solibacter usi...
ZP_00769790   72 --gvnvdadfeplyiispekRSTVSELRGLLKdvdELYLATDGDREGEAIAWHLLETlkp----riPVKRMVFHEITEPA 145  Mycobacterium ...
BAB81408      50 ---------ynpkyitirgkGELLSKLRKLAKksdKIYLATDPDREGEAISWHLANVlki---denENCRIEFNEITKDA 117  Clostridium pe...
Feature 1                
1CY7_A       149 IRQAFNKP 156  Escherichia coli
1I7D_A       142 VERAIDRL 149  Escherichia coli
1CY4_A       149 IRQAFNKP 156  Escherichia coli
NP_295097    174 IQAAIAAP 181  Deinococcus radiodurans R1
P39814       118 IKESFKHP 125  Bacillus subtilis
CAD75669     159 IQHALEDP 166  Rhodopirellula baltica SH 1
AAQ65921     117 IRAAIENP 124  Porphyromonas gingivalis W83
EAM54240     120 VEKAFEKP 127  Solibacter usitatus Ellin6076
ZP_00769790  146 IRAAAEHP 153  Mycobacterium tuberculosis F11
BAB81408     118 VKNSIKHP 125  Clostridium perfringens str. 13

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