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PDBsum entry 3o1m
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Oxidoreductase
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PDB id
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3o1m
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Oxidoreductase
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Title:
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Iron-catalyzed oxidation intermediates captured in a DNA repair dioxygenase
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Structure:
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Alpha-ketoglutarate-dependent dioxygenase alkb. Chain: a. Fragment: n-terminus 11 truncated alkb (unp residues 12 to 216). Synonym: alkylated DNA repair protein alkb. Engineered: yes. Mutation: yes. DNA (5'-d( T Ap Gp Gp Tp Ap Ap (Me6)p Ap Cp Cp Gp T)-3'). Chain: b. Engineered: yes.
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Source:
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Escherichia coli. Organism_taxid: 83333. Gene: alkb, aidd, b2212, jw2200. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: this sequence is made using solid-state DNA synthesizer.. Synthesizer.
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Resolution:
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1.75Å
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R-factor:
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0.167
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R-free:
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0.191
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Authors:
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C.Yi,G.Jia,G.Hou,Q.Dai,W.Zhang,G.Zheng,X.Jian,C.-G.Yang,Q.Cui,C.He
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Key ref:
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C.Yi
et al.
(2010).
Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase.
Nature,
468,
330-333.
PubMed id:
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Date:
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21-Jul-10
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Release date:
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17-Nov-10
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PROCHECK
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Headers
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References
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P05050
(ALKB_ECOLI) -
Alpha-ketoglutarate-dependent dioxygenase AlkB from Escherichia coli (strain K12)
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Seq:
Struc:
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216 a.a.
201 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 1 residue position (black
cross)
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A-G-G-T-A-A-ME6-A-2YR-C-G-T
12 bases
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A-A-C-G-G-T-A-T-T-A-C-C-T
13 bases
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Enzyme class:
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E.C.1.14.11.33
- Dna oxidative demethylase.
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Reaction:
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a methylated nucleobase within DNA + 2-oxoglutarate + O2 = a nucleobase within DNA + formaldehyde + succinate + CO2
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methylated nucleobase within DNA
Bound ligand (Het Group name = )
corresponds exactly
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2-oxoglutarate
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+
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O2
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=
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nucleobase within DNA
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+
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formaldehyde
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+
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succinate
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+
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CO2
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Cofactor:
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Fe cation
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Nature
468:330-333
(2010)
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PubMed id:
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Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase.
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C.Yi,
G.Jia,
G.Hou,
Q.Dai,
W.Zhang,
G.Zheng,
X.Jian,
C.G.Yang,
Q.Cui,
C.He.
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ABSTRACT
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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C.Yi,
B.Chen,
B.Qi,
W.Zhang,
G.Jia,
L.Zhang,
C.J.Li,
A.R.Dinner,
C.G.Yang,
and
C.He
(2012).
Duplex interrogation by a direct DNA repair protein in search of base damage.
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Nat Struct Mol Biol,
19,
671-676.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
