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2O59

Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glycerol pH 8.0

Functional Information from GO Data
ChainGOidnamespacecontents
A0000287molecular_functionmagnesium ion binding
A0003677molecular_functionDNA binding
A0003916molecular_functionDNA topoisomerase activity
A0003917molecular_functionDNA topoisomerase type I (single strand cut, ATP-independent) activity
A0005515molecular_functionprotein binding
A0006261biological_processDNA-templated DNA replication
A0006265biological_processDNA topological change
A0006281biological_processDNA repair
A0006310biological_processDNA recombination
A0016853molecular_functionisomerase activity
A0043597cellular_componentcytoplasmic replication fork
A0046872molecular_functionmetal ion binding
A0051304biological_processchromosome separation
A0098847molecular_functionsequence-specific single stranded DNA binding
B0000287molecular_functionmagnesium ion binding
B0003677molecular_functionDNA binding
B0003916molecular_functionDNA topoisomerase activity
B0003917molecular_functionDNA topoisomerase type I (single strand cut, ATP-independent) activity
B0005515molecular_functionprotein binding
B0006261biological_processDNA-templated DNA replication
B0006265biological_processDNA topological change
B0006281biological_processDNA repair
B0006310biological_processDNA recombination
B0016853molecular_functionisomerase activity
B0043597cellular_componentcytoplasmic replication fork
B0046872molecular_functionmetal ion binding
B0051304biological_processchromosome separation
B0098847molecular_functionsequence-specific single stranded DNA binding
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE CL A 800
ChainResidue
AARG60
ATRP61
BARG185
CDC1
DDC1

site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE CL B 801
ChainResidue
DDC1
AARG185
BARG60
BTRP61
CDC1

site_idAC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE ACY B 803
ChainResidue
BARG408
BGLN409

Functional Information from PROSITE/UniProt
site_idPS00396
Number of Residues16
DetailsTOPO_IA_1 Topoisomerase (Topo) IA-type active site signature. QkLYEthkl........ITYpRSD
ChainResidueDetails
AGLN317-ASP332

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues266
DetailsDomain: {"description":"Toprim","evidences":[{"source":"HAMAP-Rule","id":"MF_00953","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues10
DetailsRegion: {"description":"Interaction with DNA"}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues2
DetailsActive site: {"description":"O-(5'-phospho-DNA)-tyrosine intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU01383","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10574789","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00953","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues10
DetailsSite: {"description":"Interaction with DNA"}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues448
DetailsDomain: {"description":"Topo IA-type catalytic","evidences":[{"source":"PROSITE-ProRule","id":"PRU01383","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idCSA1
Number of Residues4
DetailsAnnotated By Reference To The Literature 1ecl
ChainResidueDetails
AASP103
ATYR328
AGLU7
AHIS381

site_idCSA2
Number of Residues4
DetailsAnnotated By Reference To The Literature 1ecl
ChainResidueDetails
BASP103
BTYR328
BGLU7
BHIS381

site_idCSA3
Number of Residues4
DetailsAnnotated By Reference To The Literature 1ecl
ChainResidueDetails
ATYR328
ALYS8
AGLU7
AARG330

site_idCSA4
Number of Residues4
DetailsAnnotated By Reference To The Literature 1ecl
ChainResidueDetails
BTYR328
BLYS8
BGLU7
BARG330

site_idMCSA1
Number of Residues6
DetailsM-CSA 64
ChainResidueDetails
CDT7hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
CDT8electrostatic stabiliser, hydrogen bond donor

site_idMCSA2
Number of Residues6
DetailsM-CSA 64
ChainResidueDetails
DDT7hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
DDT8electrostatic stabiliser, hydrogen bond donor

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PDB entries from 2025-07-23

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