3UXP: DNA polymerase beta

Co-crystal Structure of Rat DNA polymerase beta Mutator I260Q: Enzyme-DNA-ddTTP. Determined by X-ray diffraction at 2.72 Å resolution. Released 5 Dec 2012.

Method: X-ray diffraction
Resolution: 2.72 Å
Organism: Rattus norvegicus
Chains: 6
Atoms: 6,010
Mol. weight: 87.62 kDa
Ligands: D3T
Released: 5 Dec 2012

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

Secondary structure: helices and β-sheets

3UXP contains 39 α-helices and 22 β-strands across 2 chains. 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: 20 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	13-28	16
α-helix	34-48	15
α-helix	52-53	2
α-helix	56-60	5
α-helix	67-78	12
α-helix	84-89	6
α-helix	92-100	9
α-helix	108-116	9
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	179-182	4
β-strand	187-188	2	1
β-strand	191-196	6	2
α-helix	208-220	13
β-strand	224-230	7	2
β-strand	234-239	6	2
α-helix	250-252	3
β-strand	253-260	8	2
α-helix	262-264	3
α-helix	265-272	8
α-helix	276-284	9
β-strand	291	1	3
β-strand	300	1	3
β-strand	301	1	4
β-strand	307	1	4
α-helix	316-322	7

Chain B: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	13-28	16
α-helix	33-48	16
α-helix	56-60	5
α-helix	67-79	13
α-helix	83-88	6
α-helix	92-100	9
α-helix	109-115	7
α-helix	122-127	6
α-helix	129-131	3
α-helix	134-141	8
α-helix	143-147	5
β-strand	150-151	2	5
α-helix	152-169	18
β-strand	174-177	4	6
β-strand	187-188	2	5
β-strand	192-196	5	6
α-helix	209-220	12
β-strand	224-230	7	6
β-strand	234-239	6	6
α-helix	249-252	4
β-strand	253-259	7	6
α-helix	265-273	9
α-helix	276-285	10
β-strand	291-293	3	7
β-strand	298-300	3	7
β-strand	301	1	8
β-strand	307	1	8
α-helix	316-322	7
α-helix	325-327	3
α-helix	330-332	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase beta	A, B	protein	335	Rattus norvegicus	P06766 (AlphaFold model)
DNA 5'-d(paptpgptpgpap*g)-3'	D, P	DNA	7
DNA 5'-d(papcptpcpapcpaptp*a)-3'	E, T	DNA	9

Sequence of entity 1 (A, B), FASTA

>3UXP_1 DNA polymerase beta (chains A, B)
MSKRKAPQETLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAK
KLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIK
TLEDLRKNEDKLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGS
FRRGAESSGDMDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTLSKGETKFMGVCQ
LPSENDENEYPHRRIDIRLQPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRP
LGVTGVAGEPLPVDSEQDIFDYIQWRYREPKDRSE

Sequence of entity 2 (D, P), FASTA

>3UXP_2 DNA 5'-D(P*AP*TP*GP*TP*GP*AP*G)-3' (chains D, P)
ATGTGAG

Sequence of entity 3 (E, T), FASTA

>3UXP_3 DNA 5'-D(P*AP*CP*TP*CP*AP*CP*AP*TP*A)-3' (chains E, T)
ACTCACATA

Ligands and cofactors

ID	Name	Formula	Copies
D3T	2',3'-dideoxy-thymidine-5'-triphosphate	C10 H17 N2 O13 P3	2

Water and common crystallization additives (NA) are not listed.

Primary citation

Structural Changes in the Hydrophobic Hinge Region Adversely Affect the Activity and Fidelity of the I260Q Mutator DNA Polymerase beta. Gridley, C.L., Rangarajan, S., Firbank, S. et al. Biochemistry (2013) 52:4422-4432. DOI 10.1021/bi301368f · 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…
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…

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