Structure of PDB 6bov Chain A

Receptor sequence
>6bovA (length=270) Species: 9606 (Homo sapiens) [Search protein sequence]
ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDIL
CLQQTKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKV
SYGIGEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKG
LASRKPLVLCGNLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVP
LADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDS
KIRSKALGSDHCPITLYLAL
3D structure
PDB6bov Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches.
ChainA
Resolution1.975 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) N68 Q96 N210 N212 D283 D308 H309
Catalytic site (residue number reindexed from 1) N26 Q54 N162 N164 D235 D260 H261
Enzyme Commision number 3.1.11.2: exodeoxyribonuclease III.
3.1.21.-
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 Y171 N174 R177 N212 N222 N226 N229 F266 M271 K276 V278 W280 H309 Y123 N126 R129 N164 N174 N178 N181 F218 M223 K228 V230 W232 H261
BS02 dna A G71 R73 A74 K78 K98 G127 K224 K228 Y269 M270 G29 R31 A32 K36 K56 G85 K176 K180 Y221 M222
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003691 double-stranded telomeric DNA binding
GO:0003713 transcription coactivator activity
GO:0003714 transcription corepressor activity
GO:0003723 RNA binding
GO:0003824 catalytic activity
GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0004518 nuclease activity
GO:0004519 endonuclease activity
GO:0004520 DNA endonuclease activity
GO:0004523 RNA-DNA hybrid ribonuclease activity
GO:0004527 exonuclease activity
GO:0004528 phosphodiesterase I activity
GO:0004844 uracil DNA N-glycosylase activity
GO:0005515 protein binding
GO:0008081 phosphoric diester hydrolase activity
GO:0008296 3'-5'-DNA exonuclease activity
GO:0008309 double-stranded DNA exodeoxyribonuclease activity
GO:0008311 double-stranded DNA 3'-5' DNA exonuclease activity
GO:0008408 3'-5' exonuclease activity
GO:0016491 oxidoreductase activity
GO:0016890 site-specific endodeoxyribonuclease activity, specific for altered base
GO:0031490 chromatin DNA binding
GO:0046872 metal ion binding
GO:0052720 class II DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0090580 phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands
GO:0140431 DNA-(abasic site) binding
Biological Process
GO:0000723 telomere maintenance
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006287 base-excision repair, gap-filling
GO:0006308 DNA catabolic process
GO:0006310 DNA recombination
GO:0042981 regulation of apoptotic process
GO:0043488 regulation of mRNA stability
GO:0044029 positive regulation of gene expression via chromosomal CpG island demethylation
GO:0045454 cell redox homeostasis
GO:0045892 negative regulation of DNA-templated transcription
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0097698 telomere maintenance via base-excision repair
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum
GO:0005813 centrosome
GO:0005840 ribosome
GO:0016607 nuclear speck
GO:0048471 perinuclear region of cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6bov, PDBe:6bov, PDBj:6bov
PDBsum6bov
PubMed30082511
UniProtP27695|APEX1_HUMAN DNA repair nuclease/redox regulator APEX1 (Gene Name=APEX1)

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