Brand  (β version)

PDB ID: 1BPY

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Ligands
Code Name Style Show Link
DCT 2',3'-dideoxycytidine 5'-triphosphate PoSSuM
MG Magnesium ion PoSSuM
NA Sodium ion PoSSuM
Non-standard Residues
Code Name Show
DOC 2',3'-dideoxycytidine-5'-monophosphate
Glycosylation
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Modification
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Structure summary

Code : 1BPY   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE/DNA
Title : HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP
Release Data : 1997-06-16
Compound :
mol_id molecule chains
1 DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') T
mol_id molecule chains
2 DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*DOC)-3') P
mol_id molecule chains
3 DNA (5'-D(*GP*TP*CP*GP*G)-3') D
mol_id molecule chains synonym
4 PROTEIN (DNA POLYMERASE BETA) A POL BETA, BETA-POL
ec: 2.7.7.7
Source :
mol_id organism_scientific
1 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
2 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
3 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific organism_common expression_system
4 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:562)
cellular_location: NUCLEUS
Authors : Sawaya, M.R., Pelletier, H., Prasad, R., Wilson, S.H., Kraut, J.
Keywords : NUCLEOTIDYLTRANSFERASE, DNA REPAIR, BASE EXCISION REPAIR PATHWAY, TRANSFERASE-DNA COMPLEX
Exp. method : X-RAY DIFFRACTION ( 2.200 Å )
Citation :

Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.

Sawaya, M.R.,Prasad, R.,Wilson, S.H.  et al.
(1997)  Biochemistry  36 : 11205 - 11215

PubMed: 9287163
DOI: 10.1021/bi9703812

Characterization of the Metal Ion Binding Helix-Hairpin-Helix Motifs in Human DNA Polymerase Beta by X-Ray Structural Analysis

Pelletier, H.,Sawaya, M.R.
(1996)  Biochemistry  35 : 12778

A Structural Basis for Metal Ion Mutagenicity and Nucleotide Selectivity in Human DNA Polymerase Beta

Pelletier, H.,Sawaya, M.R.,Wolfle, W.  et al.
(1996)  Biochemistry  35 : 12762

Crystal Structures of Human DNA Polymerase Beta Complexed with DNA: Implications for Catalytic Mechanism, Processivity, and Fidelity

Pelletier, H.,Sawaya, M.R.,Wolfle, W.  et al.
(1996)  Biochemistry  35 : 12742

Crystal Structure of Rat DNA Polymerase Beta: Evidence for a Common Polymerase Mechanism

Sawaya, M.R.,Pelletier, H.,Kumar, A.  et al.
(1994)  Science  264 : 1930

Structures of Ternary Complexes of Rat DNA Polymerase Beta, a DNA Template- Primer, and ddCTP

Pelletier, H.,Sawaya, M.R.,Kumar, A.  et al.
(1994)  Science  264 : 1891

Reaction

Chain : A
UniProt : P06746 (DPOLB_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.7 -
-
a 5'-end 2'-deoxyribose-2'-deoxyribonucleotide-DNA = (2E,4S)- 4-hydroxypenten-2-al-5-phosphate + a 5'-end 5'-phospho-2'- deoxyribonucleoside-DNA + H(+) - PubMed:9572863, PubMed:9614142
-
2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'- deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho-2'- deoxyribonucleoside-DNA + H(+) 4.2.99.18 PubMed:9614142
-
Cofactor: Evidence: Note:
Mg(2+) ECO:0000269 | PubMed:9287163
Binds 2 magnesium ions per subunit.