Structure of PDB 2bpf Chain A

Receptor sequence

>2bpfA (length=324) Species: 10116 (Rattus norvegicus) [Search protein sequence]

ETLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAE
AKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGP
SAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKRIPREEMLQM
QDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSESSKQP
KLLHRVVEQLQKVRFITDTLSKGETKFMGVCQLPSENEYPHRRIDIRLIP
KDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPL
PVDSEQDIFDYIQWRYREPKDRSE

3D structure

PDB

2bpf Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP.

Chain

Resolution

2.9 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	D190 D192 D256
Catalytic site (residue number reindexed from 1)	D182 D184 D245
Enzyme Commision number	2.7.7.7: DNA-directed DNA polymerase. 4.2.99.- 4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)
BS01	dna	A	S229 K230 G231 T233 K234 R283 L287 T292 I293 N294 E295 Y296	S221 K222 G223 T225 K226 R272 L276 T281 I282 N283 E284 Y285
BS02	dna	A	T104 G105 G107 P108 A110 R254 D256 Y271	T96 G97 G99 P100 A102 R243 D245 Y260
BS03	MG	A	S180 D190 D192	S172 D182 D184
BS04	MG	A	D190 D192	D182 D184
BS05	DCT	A	R149 G179 S180 R183 G189 D190 D192 Y271 F272 G274 D276 N279	R141 G171 S172 R175 G181 D182 D184 Y260 F261 G263 D265 N268

Gene Ontology

	Molecular Function
GO:0003677	DNA binding
GO:0003684	damaged DNA binding
GO:0003887	DNA-directed DNA polymerase activity
GO:0005515	protein binding
GO:0008017	microtubule binding
GO:0016779	nucleotidyltransferase activity
GO:0016829	lyase activity
GO:0019899	enzyme binding
GO:0034061	DNA polymerase activity
GO:0046872	metal ion binding
GO:0051575	5'-deoxyribose-5-phosphate lyase activity
GO:0140078	class I DNA-(apurinic or apyrimidinic site) endonuclease activity

	Biological Process
GO:0001701	in utero embryonic development
GO:0006259	DNA metabolic process
GO:0006260	DNA replication
GO:0006281	DNA repair
GO:0006284	base-excision repair
GO:0006287	base-excision repair, gap-filling
GO:0006290	pyrimidine dimer repair
GO:0006297	nucleotide-excision repair, DNA gap filling
GO:0006303	double-strand break repair via nonhomologous end joining
GO:0006915	apoptotic process
GO:0006954	inflammatory response
GO:0006974	DNA damage response
GO:0007435	salivary gland morphogenesis
GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage
GO:0010332	response to gamma radiation
GO:0016445	somatic diversification of immunoglobulins
GO:0016446	somatic hypermutation of immunoglobulin genes
GO:0045471	response to ethanol
GO:0048535	lymph node development
GO:0048536	spleen development
GO:0048872	homeostasis of number of cells
GO:0051402	neuron apoptotic process
GO:0055093	response to hyperoxia
GO:0071707	immunoglobulin heavy chain V-D-J recombination
GO:0071897	DNA biosynthetic process

	Cellular Component
GO:0005634	nucleus
GO:0005737	cytoplasm
GO:0005874	microtubule
GO:0005876	spindle microtubule
GO:0032991	protein-containing complex

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:2bpf, PDBe:2bpf, PDBj:2bpf
PDBsum	2bpf
PubMed	7516580
UniProt	P06766\|DPOLB_RAT DNA polymerase beta (Gene Name=Polb)

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