Brand  (β version)

PDB ID: 3KHH

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Ligands
Code Name Style Show Link
DGT 2'-deoxyguanosine-5'-triphosphate PoSSuM
CA Calcium ion PoSSuM
AF 2-aminofluorene PoSSuM
Non-standard Residues
Code Name Show
DOC 2',3'-dideoxycytidine-5'-monophosphate
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 3KHH   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE/DNA
Title : Dpo4 extension ternary complex with a C base opposite the 2-aminofluorene-guanine [AF]G lesion
Release Data : 2010-02-16
Compound :
mol_id molecule chains synonym
1 DNA polymerase IV A,B 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*(DOC))-3' D,H
other_details: DNA primer strand (Dideoxy-terminated at the 3'-end)
mol_id molecule chains
3 5'-D(*CP*CP*TP*A*AP*CP*GP*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3' E,J
other_details: DNA [AF]G-modified template strand
Source :
mol_id organism_scientific expression_system
1 Sulfolobus solfataricus P2  (taxid:273057) Escherichia coli  (taxid:562)
strain: P2 / DSM 1617 / JCM 11322
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 strand (Dideoxy-terminated at the 3'-end)
mol_id organism_scientific
3
synthetic: yes
other_details: DNA [AF]G-modified template strand
Authors : Rechkoblit, O., Malinina, L., Patel, D.J.
Keywords : Lesion bypass, DNA polymerase, Y-family polymerase, 2-aminofluorene, semi-targeted mutagenesis, 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 ( 2.70 Å )
Citation :

Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4.

Rechkoblit, O.,Kolbanovskiy, A.,Malinina, L.  et al.
(2010)  Nat.Struct.Mol.Biol.  17 : 379 - 388

PubMed: 20154704
DOI: 10.1038/nsmb.1771

Reaction

Chain : A, B
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.