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: 17-Jan-2013
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 KALVIVESPAKAKTINKYLG.[ 2].YVVKSSVGHIRDLP.[51].EKVVSELKQLAE.[3].HIYLATDLDREGEAIAW 123  Escherichia coli
1I7D_A         1 MRLFIAEKPSLARAIADVLP.[15].QVVTWCIGHLLEQA.[32].TKQLNVIKRFLH.[3].EIVHAGDPDREGQLLVD 113  Escherichia coli
1CY4_A         5 KALVIVESPAKAKTINKYLG.[ 2].YVVKSSVGHIRDLP.[51].EKVVSELKQLAE.[3].HIYLATDLDREGEAIAW 123  Escherichia coli
NP_295097     46 KTLVIVESPAKAKTIEKYLG.[ 2].YAVESSVGHIRDLP.[36].KQKVAQLRKLAA.[3].EIILATDDDREGESIAW 149  Deinococcus radiodu...
P39814         3 DYLVIVESPAKAKTIERYLG.[ 2].YKVKASMGHVRDLP.[22].GPVLKELKTAAK.[3].KVYLAADPDREGEAIAW 92   Bacillus subtilis
CAD75669      31 KSLVIVESPAKARTISKFLG.[ 2].YQVEASVGHVRDLP.[36].KKQVDKLKAALK.[3].SLYLATDEDREGEAISW 134  Rhodopirellula balt...
AAQ65921       2 KNLVIVESPAKAKTIGRFLG.[ 2].YTVLSSYGHIRDLK.[22].RPVVKELKSQAD.[3].FIWLASDEDREGEAIAW 91   Porphyromonas gingi...
EAM54240       3 KALVIVESPAKAKTINKYLG.[ 2].YVVKASLGHIKDLP.[22].KKLMGELRSAAK.[3].QIYLAADPDREGEAICF 92   Solibacter usitatus...
ZP_00769790   18 RRLVIVESPTKARKLASYLG.[ 2].YIVESSRGHIRDLP.[36].RSTVSELRGLLK.[3].ELYLATDGDREGEAIAW 121  Mycobacterium tuber...
BAB81408       3 QKLVIVESPAKAKTIEKYLG.[ 2].YVVEASMGHVRDLP.[22].GELLSKLRKLAK.[3].KIYLATDPDREGEAISW 92   Clostridium perfrin...

Feature 1                                        
1CY7_A       124 HLREV.[6].RYSRVVFNEITKNAIRQAFNKP 156  Escherichia coli
1I7D_A       114 EVLDY.[9].QVQRCLINDLNPQAVERAIDRL 149  Escherichia coli
1CY4_A       124 HLREV.[6].RYSRVVFNEITKNAIRQAFNKP 156  Escherichia coli
NP_295097    150 HLYQE.[5].PVKRMVFHEITREAIQAAIAAP 181  Deinococcus radiodurans R1
P39814        93 HLAHS.[6].SDCRVVFNEITKDAIKESFKHP 125  Bacillus subtilis
CAD75669     135 HLFEL.[5].PVHRLVFHEITKEAIQHALEDP 166  Rhodopirellula baltica SH 1
AAQ65921      92 HLYEA.[6].QTKRIVFHEITETAIRAAIENP 124  Porphyromonas gingivalis W83
EAM54240      93 HLQEE.[8].AFFRVMFNEITKKAVEKAFEKP 127  Solibacter usitatus Ellin6076
ZP_00769790  122 HLLET.[5].PVKRMVFHEITEPAIRAAAEHP 153  Mycobacterium tuberculosis F11
BAB81408      93 HLANV.[6].ENCRIEFNEITKDAVKNSIKHP 125  Clostridium perfringens str. 13

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