1BPB: DNA polymerase beta

Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. Determined by X-ray diffraction at 2.3 Å resolution. Released 22 Jun 1994.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Rattus norvegicus
Chains: 1
Atoms: 2,024
Mol. weight: 28.77 kDa
Released: 22 Jun 1994

Explore 1BPB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1BPB contains 16 α-helices and 11 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	94-100	7
α-helix	108-114	7
α-helix	122-127	6
α-helix	129-131	3
α-helix	134-141	8
α-helix	145-147	3
α-helix	149	1
β-strand	150-151	2	1
α-helix	152-169	18
β-strand	174-177	4	2
α-helix	179-182	4
β-strand	187-188	2	1
β-strand	191-196	6	2
α-helix	208-221	14
β-strand	224-230	7	2
β-strand	234-239	6	2
α-helix	250-252	3
β-strand	253-259	7	2
α-helix	262-264	3
α-helix	265-273	9
α-helix	276-288	13
β-strand	291-293	3	3
β-strand	298-300	3	3
β-strand	302	1	4
β-strand	305	1	4
α-helix	316-322	7
α-helix	330-332	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase beta	A	protein	248	Rattus norvegicus	P06766 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1BPB_1 DNA POLYMERASE BETA (chains A)
IRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFE
KRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSESSKQ
PKLLHRVVEQLQKVRFITDTLSKGETKFMGVCQLPSENDENEYPHRRIDIRLIPKDQYYC
GVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEQDIFDYIQWRY
REPKDRSE

Primary citation

Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. Sawaya, M.R., Pelletier, H., Kumar, A. et al. Science (1994) 264:1930-1935. PubMed

Other PDB entries of the same protein (UniProt P06766 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VAN 2.1 Å, Nucleotidyl Transfer Mechanism of Mismatched dNTP Incorporation by DNA Polymerase b by…
3UXO 2.1 Å, Crystal Structure of Rat DNA Polymerase Beta Mutator I260Q Apoenzyme
3V7J 2.25 Å, Co-crystal structure of Wild Type Rat polymerase beta: Enzyme-DNA binary complex
3V7K 2.27 Å, Co-crystal structure of K72E variant of rat polymerase beta: Enzyme-DNA binary complex
1RPL 2.3 Å, 2.3 Å crystal structure of the catalytic domain of DNA polymerase beta
1ZQW 2.3 Å, DNA polymerase beta (pol B) (E.C.2.7.7.7), 31-kd domain; soaked in the presence of cscl…
1ZQY 2.3 Å, DNA polymerase beta (pol B) (E.C.2.7.7.7), 31-kd domain; soaked in the presence of MGCL2…
3LQC 2.35 Å, X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta Palm thumb domain
1JN3 2.35 Å, Fidelity properties and structure of M282L mutator mutant of DNA polymerase: subtle…
3V72 2.49 Å, Crystal Structure of Rat DNA polymerase beta Mutator E295K: Enzyme-dsDNA
1ZQX 2.5 Å, DNA polymerase beta (pol B) (E.C.2.7.7.7), 31-kd domain; soaked in the presence of kcl…
3UXN 2.5 Å, Crystal Structure of Rat DNA Polymerase Beta, Wild Type Apoenzyme

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