Brand  (β version)

PDB ID: 3GII

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Ligands
Code Name Style Show Link
CA Calcium ion PoSSuM
DGT 2'-deoxyguanosine-5'-triphosphate PoSSuM
NA Sodium ion PoSSuM
Non-standard Residues
Code Name Show
2DA 2',3'-dideoxyadenosine-5'-monophosphate
8OG 8-oxo-2'-deoxy-guanosine-5'-monophosphate
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 3GII   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE/DNA
Title : Dpo4 extension ternary complex with disordered A opposite an oxoG in anti conformation
Release Data : 2009-05-19
Compound :
mol_id molecule chains synonym
1 DNA polymerase IV A Pol IV
ec: 2.7.7.7
mol_id molecule chains
2 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3' D
mol_id molecule chains
3 5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3' E
Source :
mol_id organism_scientific expression_system
1 Sulfolobus solfataricus P2  (taxid:273057) Escherichia coli  (taxid:562)
strain: P2 / DSM 1617 / JCM 11322
atcc: 35092
gene: dbh, dpo4, SSO2448
expression_system_strain: BL21(DE3)-RIL(STRATAGENE)
expression_system_vector_type: Plasmid
expression_system_plasmid: pET28a
mol_id organism_scientific
2
synthetic: yes
other_details: DNA primer
mol_id organism_scientific
3
synthetic: yes
other_details: OXOG-modified template strand
Authors : Rechkoblit, O., Malinina, L., Patel, D.J.
Keywords : DNA POLYMERASE, 8-OXOGUANINE, Y-FAMILY, LESION BYPASS, DNA damage, DNA repair, DNA replication, DNA-binding, DNA-directed DNA polymerase, Magnesium, Metal-binding, Mutator protein, Nucleotidyltransferase, Transferase, TRANSFERASE-DNA COMPLEX
Exp. method : X-RAY DIFFRACTION ( 2.600 Å )
Citation :

Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases.

Rechkoblit, O.,Malinina, L.,Cheng, Y.  et al.
(2009)  Structure  17 : 725 - 736

PubMed: 19446528
DOI: 10.1016/j.str.2009.03.011

Reaction

Chain : A
UniProt : Q97W02 (DPO4_SACS2)
Reaction: EC: Evidence:
Physiological Direction:
DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.7 -
-
Cofactor: Evidence: Note:
Mg(2+) - Binds 2 magnesium ions per subunit.