Structure of PDB 6fbu Chain A

Receptor sequence
>6fbuA (length=254) Species: 83333 (Escherichia coli K-12) [Search protein sequence]
PQGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETR
GKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTI
LLYSASDIEMLRPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRN
RQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHA
LLEIPRFSYATRGQALFRFKVFHRDGEPCERCGSIIEKTTLSSRPFYWCP
GCQH
3D structure
PDB6fbu Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate
ChainA
Resolution2.0 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)		 Binding affinity
BS01 dna A Y71 R87 V88 R90 S104 S106 Y71 R87 V88 R90 S104 S106
BS02 dna A P1 Q2 K52 H67 Q69 L70 F121 R124 Q160 N168 Y169 R252 P253 P1 Q2 K52 H67 Q69 L70 F121 R124 Q160 N168 Y169 R244 P245
BS03 ZN A C237 C240 C257 C260 C229 C232 C249 C252
Gene Ontology
Molecular Function
GO:0000703 oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0016829 lyase activity
GO:0019104 DNA N-glycosylase activity
GO:0046872 metal ion binding
GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity
Biological Process
GO:0006281 DNA repair
GO:0006284 base-excision repair

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Molecular Function
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Biological Process
External links
PDB RCSB:6fbu, PDBe:6fbu, PDBj:6fbu
PDBsum6fbu
PubMed
UniProtP50465|END8_ECOLI Endonuclease 8 (Gene Name=nei)

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