Structure of PDB 4iem Chain B

Receptor sequence
>4iemB (length=275) Species: 9606 (Homo sapiens) [Search protein sequence]
LYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILC
LQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVS
YGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFR
KFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGEL
LQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLP
ALCDSKIRSKALGSDHCPITLYLAL
3D structure
PDB4iem Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV DNA Repair Enzymes.
ChainB
Resolution2.3936 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) D70 E96 N212 D283 D308
Catalytic site (residue number reindexed from 1) D27 E53 N169 D240 D265
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 B E96 Y128 Y171 E53 Y85 Y128
BS02 dna B Y171 N174 R177 D210 N212 N229 F266 T268 M270 M271 V278 W280 H309 Y128 N131 R134 D167 N169 N186 F223 T225 M227 M228 V235 W237 H266
BS03 dna B G71 R73 A74 K78 L179 K228 Y269 M270 M271 G28 R30 A31 K35 L136 K185 Y226 M227 M228
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4iem, PDBe:4iem, PDBj:4iem
PDBsum4iem
PubMed23355472
UniProtP27695|APEX1_HUMAN DNA repair nuclease/redox regulator APEX1 (Gene Name=APEX1)

[Back to BioLiP]