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PDBsum entry 1odg
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Contents |
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* Residue conservation analysis
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PDB id:
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Hydrolase
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Title:
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Very-short-patch DNA repair endonuclease bound to its reaction product site
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Structure:
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DNA mismatch endonuclease. Chain: a. Synonym: very short patch repair protein, vsr mismatch endonuclease, v.Ecokdcm, vsr, b1960. Engineered: yes. 5'-d( Tp Ap Gp Gp Cp 5Cm Tp Gp Gp Ap Tp Cp)-3'. Chain: f, w
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Source:
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Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Organism_taxid: 562
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Biol. unit:
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Trimer (from PDB file)
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Resolution:
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2.80Å
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R-factor:
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0.287
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R-free:
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0.356
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Authors:
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K.A.Bunting,S.M.Roe,A.Headley,T.Brown,R.Savva,L.H.Pearl
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Key ref:
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K.A.Bunting
et al.
(2003).
Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix.
Nucleic Acids Res,
31,
1633-1639.
PubMed id:
DOI:
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Date:
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19-Feb-03
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Release date:
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13-Mar-03
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PROCHECK
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Headers
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References
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P09184
(VSR_ECOLI) -
DNA mismatch endonuclease Vsr from Escherichia coli (strain K12)
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Seq:
Struc:
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156 a.a.
134 a.a.
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Key: |
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Secondary structure |
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CATH domain |
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T-A-G-G-C-5CM-T-G-G-A-T-C
12 bases
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T-A-G-G-C-5CM-T-G-G-A-T-C
12 bases
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DOI no:
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Nucleic Acids Res
31:1633-1639
(2003)
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PubMed id:
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Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix.
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K.A.Bunting,
S.M.Roe,
A.Headley,
T.Brown,
R.Savva,
L.H.Pearl.
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ABSTRACT
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Very-short-patch repair (Vsr) enzymes occur in a variety of bacteria, where they
initiate nucleotide excision repair of G:T mismatches arising by deamination of
5-methyl-cytosines in specific regulatory sequences. We have now determined the
structure of the archetypal dcm-Vsr endonuclease from Escherichia coli bound to
the cleaved authentic hemi-deaminated/hemi-methylated dcm sequence 5'-C-OH-3'
5'-p-T-p-A-p-G-p-G-3'/3'-G-p-G-p-T-p(Me5)C-p-C formed by self-assembly of a
12mer oligonucleotide into a continuous nicked DNA superhelix. The structure
reveals the presence of a Hoogsteen base pair within the deaminated recognition
sequence and the substantial distortions of the DNA that accompany Vsr binding
to product sites.
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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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W.Yang
(2011).
Nucleases: diversity of structure, function and mechanism.
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Q Rev Biophys,
44,
1.
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L.Mones,
I.Simon,
and
M.Fuxreiter
(2007).
Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism.
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Biol Chem,
388,
73-78.
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J.R.Horton,
X.Zhang,
R.Maunus,
Z.Yang,
G.G.Wilson,
R.J.Roberts,
and
X.Cheng
(2006).
DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.
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Nucleic Acids Res,
34,
939-948.
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PDB codes:
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D.J.Rigden
(2005).
An inactivated nuclease-like domain in RecC with novel function: implications for evolution.
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BMC Struct Biol,
5,
9.
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J.L.Campos,
L.Urpí,
T.Sanmartín,
C.Gouyette,
and
J.A.Subirana
(2005).
DNA coiled coils.
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Proc Natl Acad Sci U S A,
102,
3663-3666.
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H.Ling,
F.Boudsocq,
B.S.Plosky,
R.Woodgate,
and
W.Yang
(2003).
Replication of a cis-syn thymine dimer at atomic resolution.
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Nature,
424,
1083-1087.
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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
