Structure of PDB 1yqm Chain A

Receptor sequence

>1yqmA (length=314) Species: 9606 (Homo sapiens) [Search protein sequence]

SEFGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGV
LADQVWTLTQTEEQLHCTVYRSQASRPTPDELEAVRKYFQLDVTLAQLYH
HWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSCNNIARITGMVER
LCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSAS
ARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTQVADCICLMALDK
PQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGPYA
GWAQAVLFSADLRQ

3D structure

PDB

1yqm Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.

Chain

Resolution

2.5 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

3.2.2.-
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	R154 R197 G202 Y203 R204 Q287	R143 R186 G191 Y192 R193 Q276
BS02	dna	A	S148 C149 N150 N151 I152 Y203 Y207 G245 G247 Q249 V250 M257 P266 D268 H270 Q315 F319	S137 C138 N139 N140 I141 Y192 Y196 G234 G236 Q238 V239 M246 P255 D257 H259 Q304 F308
BS03	CA	A	C241 L243 V246	C230 L232 V235

Gene Ontology

	Molecular Function
GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding
GO:0003677	DNA binding
GO:0003684	damaged DNA binding
GO:0003824	catalytic activity
GO:0004519	endonuclease activity
GO:0005515	protein binding
GO:0008017	microtubule binding
GO:0008534	oxidized purine nucleobase lesion DNA N-glycosylase activity
GO:0016798	hydrolase activity, acting on glycosyl bonds
GO:0016829	lyase activity
GO:0019104	DNA N-glycosylase activity
GO:0019899	enzyme binding
GO:0032357	oxidized purine DNA binding
GO:0034039	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
GO:0140078	class I DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0140097	catalytic activity, acting on DNA

	Biological Process
GO:0006281	DNA repair
GO:0006284	base-excision repair
GO:0006285	base-excision repair, AP site formation
GO:0006289	nucleotide-excision repair
GO:0006355	regulation of DNA-templated transcription
GO:0006974	DNA damage response
GO:0006979	response to oxidative stress
GO:0009314	response to radiation
GO:0009410	response to xenobiotic stimulus
GO:0009416	response to light stimulus
GO:0032355	response to estradiol
GO:0034614	cellular response to reactive oxygen species
GO:0043066	negative regulation of apoptotic process
GO:0044029	positive regulation of gene expression via chromosomal CpG island demethylation
GO:0045007	depurination
GO:0045008	depyrimidination
GO:0045471	response to ethanol
GO:0045944	positive regulation of transcription by RNA polymerase II
GO:0051593	response to folic acid
GO:0071276	cellular response to cadmium ion
GO:1901291	negative regulation of double-strand break repair via single-strand annealing

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005739	mitochondrion
GO:0005759	mitochondrial matrix
GO:0005829	cytosol
GO:0016363	nuclear matrix
GO:0016607	nuclear speck
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:1yqm, PDBe:1yqm, PDBj:1yqm
PDBsum	1yqm
PubMed	15800616
UniProt	O15527\|OGG1_HUMAN N-glycosylase/DNA lyase (Gene Name=OGG1)

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