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PDBsum entry 4cis
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PDB id:
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Hydrolase
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Title:
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Structure of mutm in complex with carbocyclic 8-oxo-g containing DNA
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Structure:
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Formamidopyrimidin DNA glycosylase. Chain: a, b. Synonym: fapy-DNA glycosylase, DNA-(apurinic or apyrimidinic site) lyase mutm, formamidopyrimidin DNA glycosylase. Engineered: yes. DNA. Chain: c. Engineered: yes. DNA.
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Source:
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Lactococcus lactis subsp. Cremoris. Organism_taxid: 1359. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630
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Resolution:
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2.05Å
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R-factor:
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0.215
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R-free:
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0.239
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Authors:
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S.Schneider,K.Sadeghian,D.Flaig,I.D.Blank,R.Strasser,D.Stathis, M.Winnacker,T.Carell,C.Ochsenfeld
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Key ref:
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K.Sadeghian
et al.
(2014).
Ribose-protonated DNA base excision repair: a combined theoretical and experimental study.
Angew Chem Int Ed Engl,
53,
10044-10048.
PubMed id:
DOI:
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Date:
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15-Dec-13
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Release date:
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04-Jun-14
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PROCHECK
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Headers
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References
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Q031W6
(Q031W6_LACLS) -
Formamidopyrimidine-DNA glycosylase from Lactococcus lactis subsp. cremoris (strain SK11)
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Seq:
Struc:
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272 a.a.
263 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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*
PDB and UniProt seqs differ
at 4 residue positions (black
crosses)
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G-C-G-A-G-A-A-A-C-A-A-A-G-A
14 bases
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C-T-C-T-T-T-68Z-T-T-T-C-T-C-G
14 bases
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Enzyme class 1:
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E.C.3.2.2.23
- DNA-formamidopyrimidine glycosylase.
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Reaction:
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Hydrolysis of DNA containing ring-opened N(7)-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimide.
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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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Angew Chem Int Ed Engl
53:10044-10048
(2014)
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PubMed id:
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Ribose-protonated DNA base excision repair: a combined theoretical and experimental study.
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K.Sadeghian,
D.Flaig,
I.D.Blank,
S.Schneider,
R.Strasser,
D.Stathis,
M.Winnacker,
T.Carell,
C.Ochsenfeld.
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ABSTRACT
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Living organisms protect the genome against external influences by recognizing
and repairing damaged DNA. A common source of gene mutation is the oxidized
guanine, which undergoes base excision repair through cleavage of the glycosidic
bond between the ribose and the nucleobase of the lesion. We unravel the repair
mechanism utilized by bacterial glycosylase, MutM, using quantum-chemical
calculations involving more than 1000 atoms of the catalytic site. In contrast
to the base-protonated pathway currently favored in the literature, we show that
the initial protonation of the lesion's ribose paves the way for an almost
barrier-free glycosidic cleavage. The combination of theoretical and
experimental data provides further insight into the selectivity and
discrimination of MutM's binding site toward various substrates.
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Links
