Structure of PDB 1bpy Chain A

Receptor sequence

>1bpyA (length=326) Species: 9606 (Homo sapiens) [Search protein sequence]

TLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEA
KKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPS
AARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQ
DIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPK
LLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRL
IPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGE
PLPVDSEKDIFDYIQWKYREPKDRSE

3D structure

PDB

1bpy Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.

Chain

Resolution

2.2 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)	D181 D183 D247
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	H34 S229 K230 G231 T233 K234 R258 K280 R283 N294 E295	H25 S220 K221 G222 T224 K225 R249 K271 R274 N285 E286
BS02	dna	A	S104 G105 G107 P108 S109 A110 M236 R254 D256 Y271	S95 G96 G98 P99 S100 A101 M227 R245 D247 Y262
BS03	dna	A	H34 K35 A38 Y39 P63 G64 V65 G66 K68 I69	H25 K26 A29 Y30 P54 G55 V56 G57 K59 I60
BS04	MG	A	D190 D192	D181 D183
BS05	MG	A	D190 D192 D256	D181 D183 D247
BS06	DCT	A	G179 S180 R183 G189 D190 D192 F272 G274 D276	G170 S171 R174 G180 D181 D183 F263 G265 D267

Gene Ontology

	Molecular Function
GO:0003677	DNA binding
GO:0003684	damaged DNA binding
GO:0003887	DNA-directed DNA polymerase activity
GO:0003906	DNA-(apurinic or apyrimidinic site) endonuclease 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:0006261	DNA-templated 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:0005654	nucleoplasm
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:1bpy, PDBe:1bpy, PDBj:1bpy
PDBsum	1bpy
PubMed	9287163
UniProt	P06746\|DPOLB_HUMAN DNA polymerase beta (Gene Name=POLB)

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