Structure of PDB 5vrw Chain A

Receptor sequence

>5vrwA (length=325) Species: 9606 (Homo sapiens) [Search protein sequence]

ETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAE
AKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGP
SAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQM
QDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESQPKL
LHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLI
PKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEP
LPVDSEKDIFDYIQWKYREPKDRSE

3D structure

PDB

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

Chain

Resolution

2.58 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 D246
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)	Binding affinity
BS01	dna	A	H34 K230 G231 T233 K234 R258 Y271 R283 L287 T292 I293 N294 E295 Y296	H26 K220 G221 T223 K224 R248 Y261 R273 L277 T282 I283 N284 E285 Y286
BS02	dna	A	S104 G105 G107 P108 S109 A110 R254 D256 Y271	S96 G97 G99 P100 S101 A102 R244 D246 Y261
BS03	dna	A	K35 Y39 G64 G66 K68 I69	K27 Y31 G56 G58 K60 I61
BS04	CA	A	D190 D192 D256	D182 D184 D246
BS05	CA	A	T101 V103 I106	T93 V95 I98
BS06	TTP	A	S180 G189 D190 D192 Y271 F272 T273 G274 D276 N279	S172 G181 D182 D184 Y261 F262 T263 G264 D266 N269	BindingDB: IC50=1400nM
BS07	CA	A	K60 L62 V65	K52 L54 V57
BS08	CA	A	D190 D192	D182 D184
BS09	CA	A	D314 D318	D304 D308

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

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