3V7K: DNA polymerase beta

Co-crystal structure of K72E variant of rat polymerase beta: Enzyme-DNA binary complex. Determined by X-ray diffraction at 2.27 Å resolution. Released 16 Jan 2013.

Method: X-ray diffraction
Resolution: 2.27 Å
Organism: Rattus norvegicus
Chains: 3
Atoms: 3,181
Mol. weight: 44.93 kDa
Released: 16 Jan 2013

Explore 3V7K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V7K 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	13-28	16
α-helix	33-48	16
α-helix	56-60	5
α-helix	67-78	12
α-helix	83-90	8
α-helix	92-101	10
α-helix	108-116	9
α-helix	122-126	5
α-helix	129-131	3
α-helix	134-141	8
α-helix	145-147	3
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	209-220	12
β-strand	224-230	7	2
β-strand	234-239	6	2
α-helix	241-243	3
α-helix	248-252	5
β-strand	253-259	7	2
α-helix	262-264	3
α-helix	265-273	9
α-helix	276-289	14
β-strand	291-293	3	3
β-strand	298-300	3	3
α-helix	310-312	3
α-helix	316-322	7
α-helix	326-329	4
α-helix	330-332	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase beta	A	protein	340	Rattus norvegicus	P06766 (AlphaFold model)
DNA (5'-d(paptpgptpgpapgpt)-3')	P	DNA	8
DNA (5'-d(pcpapapapcptpcpapcpap*a)-3')	T	DNA	11

Sequence of entity 1 (A), FASTA

>3V7K_1 DNA polymerase beta (chains A)
MGHHHHHHRKAPQETLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKS
GAEAKKLPGVGTKIAEEIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLV
DEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIA
TVCGSFRRGAESSGDMDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTLSKGETKF
MGVCQLPSENDENEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINE
YTIRPLGVTGVAGEPLPVDSEQDIFDYIQWRYREPKDRSE

Sequence of entity 2 (P), FASTA

>3V7K_2 DNA (5'-D(P*AP*TP*GP*TP*GP*AP*GP*T)-3') (chains P)
ATGTGAGT

Sequence of entity 3 (T), FASTA

>3V7K_3 DNA (5'-D(P*CP*AP*AP*AP*CP*TP*CP*AP*CP*AP*A)-3') (chains T)
CAAACTCACAA

Primary citation

Crystallographic studies of K72E mutant DNA polymerase explain loss of lyase function and reveal changes in the overall conformational state of the polymerase domain. Rangarajan, S., Gridley, C.L., Firbank, S. et al. To be published.

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
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…
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

Browse structure collections

About this viewer

MolViewer shows 3V7K directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.