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PDBsum entry 5itx
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DNA binding protein/DNA
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PDB id
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5itx
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PDB id:
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DNA binding protein/DNA
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Title:
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Crystal structure of human neil1(p2g r242k) bound to duplex DNA containing thymine glycol
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Structure:
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Endonuclease 8-like 1. Chain: a, b. Synonym: DNA glycosylase/ap lyase neil1,DNA-(apurinic or apyrimidinic site) lyase neil1,endonuclease viii-like 1,fpg1,nei homolog 1,neh1, nei-like protein 1. Engineered: yes. DNA (26-mer). Chain: d, c, f. Engineered: yes.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: neil1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Unidentified. Organism_taxid: 32644.
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Resolution:
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2.65Å
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R-factor:
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0.194
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R-free:
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0.235
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Authors:
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C.Zhu,L.Lu,J.Zhang,Z.Yue,J.Song,S.Zong,M.Liu,O.Stovicek,Y.Gao,C.Yi
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Key ref:
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C.Zhu
et al.
(2016).
Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair.
Proc Natl Acad Sci U S A,
113,
7792-7797.
PubMed id:
DOI:
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Date:
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17-Mar-16
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Release date:
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06-Jul-16
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PROCHECK
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Headers
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References
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Q96FI4
(NEIL1_HUMAN) -
Endonuclease 8-like 1 from Homo sapiens
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Seq:
Struc:
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390 a.a.
264 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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C-G-T-C-C-A-CTG-G-T-C-T-A-C-T-A-G-A-C-C-T-G-G-A-C-G-G
26 bases
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C-G-T-C-C-A-CTG-G-T-C-T-A-C-T-A-G-A-C-C-T-G-G-A-C-G-G
26 bases
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C-G-T-C-C-A-CTG-G-T-C-T-A-C-T-A-G-A-C-C-T-G-G-A-C-G-G
26 bases
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Enzyme class 1:
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E.C.3.2.2.-
- ?????
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Enzyme class 2:
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E.C.4.2.99.18
- DNA-(apurinic or apyrimidinic site) lyase.
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Reaction:
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2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H+
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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DOI no:
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Proc Natl Acad Sci U S A
113:7792-7797
(2016)
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PubMed id:
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Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair.
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C.Zhu,
L.Lu,
J.Zhang,
Z.Yue,
J.Song,
S.Zong,
M.Liu,
O.Stovicek,
Y.Q.Gao,
C.Yi.
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ABSTRACT
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NEIL1 (Nei-like 1) is a DNA repair glycosylase guarding the mammalian genome
against oxidized DNA bases. As the first enzymes in the base-excision repair
pathway, glycosylases must recognize the cognate substrates and catalyze their
excision. Here we present crystal structures of human NEIL1 bound to a range of
duplex DNA. Together with computational and biochemical analyses, our results
suggest that NEIL1 promotes tautomerization of thymine glycol (Tg)-a preferred
substrate-for optimal binding in its active site. Moreover, this tautomerization
event also facilitates NEIL1-catalyzed Tg excision. To our knowledge, the
present example represents the first documented case of enzyme-promoted
tautomerization for efficient substrate recognition and catalysis in an
enzyme-catalyzed reaction.
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Links
