Structure of PDB 5vs0 Chain A

Receptor sequence

>5vs0A (length=326) Species: 9606 (Homo sapiens) [Search protein sequence]

TLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEA
KKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPS
AARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQ
DIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPK
LLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRL
IPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGE
PLPVDSEKDIFDYIQWKYREPKDRSE

3D structure

PDB

5vs0 Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.

Chain

Resolution

2.1 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	K35 A38 Y39 P63 G64 V65 G66 K68 I69	K26 A29 Y30 P54 G55 V56 G57 K59 I60
BS02	dna	A	S104 G105 G107 P108 S109 A110 D190 D192 R254 D256 Y271 T273 G274 D276 N279	S95 G96 G98 P99 S100 A101 D181 D183 R245 D247 Y262 T264 G265 D267 N270
BS03	dna	A	H34 S229 K230 G231 T233 K234 K280 R283 L287 T292 N294 E295 Y296	H25 S220 K221 G222 T224 K225 K271 R274 L278 T283 N285 E286 Y287
BS04	MG	A	D190 D192	D181 D183
BS05	MG	A	D190 D192 D256	D181 D183 D247
BS06	MG	A	T101 V103 I106	T92 V94 I97
BS07	MG	A	K60 L62 V65	K51 L53 V56

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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:5vs0, PDBe:5vs0, PDBj:5vs0
PDBsum	5vs0
PubMed	28682600
UniProt	P06746\|DPOLB_HUMAN DNA polymerase beta (Gene Name=POLB)

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