3V72: DNA polymerase beta

Crystal Structure of Rat DNA polymerase beta Mutator E295K: Enzyme-dsDNA. Determined by X-ray diffraction at 2.49 Å resolution. Released 4 Jul 2012.

Method: X-ray diffraction
Resolution: 2.49 Å
Organism: Rattus norvegicus
Chains: 3
Atoms: 3,100
Mol. weight: 43.98 kDa
Released: 4 Jul 2012

Explore 3V72 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V72 contains 23 α-helices and 9 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: 23 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	13-25	13
α-helix	26-30	5
α-helix	33-47	15
α-helix	56-60	5
α-helix	67-79	13
α-helix	83-90	8
α-helix	92-100	9
α-helix	108-117	10
α-helix	122-126	5
α-helix	129-131	3
α-helix	134-141	8
α-helix	143-147	5
β-strand	150-151	2	1
α-helix	152-169	18
β-strand	174-177	4	2
α-helix	180-183	4
β-strand	187-188	2	1
β-strand	191-196	6	2
α-helix	209-220	12
β-strand	224-230	7	2
β-strand	234-239	6	2
α-helix	249-252	4
β-strand	253-259	7	2
α-helix	262-264	3
α-helix	265-271	7
α-helix	276-288	13
β-strand	291-293	3	3
β-strand	298-300	3	3
α-helix	301-302	2
α-helix	310-312	3
α-helix	316-322	7
α-helix	330-333	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase beta	A	protein	335	Rattus norvegicus	P06766 (AlphaFold model)
DNA 5'-d(paptpgptpgpapgpt)-3'	P	DNA	8
DNA 5'-d(papapapcptpcpapcpapt)-3'	T	DNA	10

Sequence of entity 1 (A), FASTA

>3V72_1 DNA polymerase beta (chains A)
MSKRKAPQETLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAK
KLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIK
TLEDLRKNEDKLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGS
FRRGAESSGDMDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTLSKGETKFMGVCQ
LPSENDENEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINKYTIRP
LGVTGVAGEPLPVDSEQDIFDYIQWRYREPKDRSE

Sequence of entity 2 (P), FASTA

>3V72_2 DNA 5'-D(P*AP*TP*GP*TP*GP*AP*GP*T)-3' (chains P)
ATGTGAGT

Sequence of entity 3 (T), FASTA

>3V72_3 DNA 5'-D(P*AP*AP*AP*CP*TP*CP*AP*CP*AP*T)-3' (chains T)
AAACTCACAT

Primary citation

Unfavorable Electrostatic and Steric Interactions in DNA Polymerase beta E295K Mutant Interfere with the Enzyme s Pathway. Li, Y., Gridley, C.L., Jaeger, J. et al. J Am Chem Soc (2012) 134:9999-10010. DOI 10.1021/ja300361r · 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
1BPB 2.3 Å, Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism
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…
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

Browse structure collections

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