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PDBsum entry 1lqm
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Hydrolase/hydrolase inhibitor
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PDB id
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1lqm
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Domain closure and action of uracil DNA glycosylase (udg): structures of new crystal forms containing the escherichia coli enzyme and a comparative study of the known structures involving udg.
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Authors
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K.Saikrishnan,
M.Bidya sagar,
R.Ravishankar,
S.Roy,
K.Purnapatre,
P.Handa,
U.Varshney,
M.Vijayan.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2002,
58,
1269-1276.
[DOI no: ]
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PubMed id
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Abstract
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The structures of a new crystal form of free Escherichia coli uracil DNA
glycosylase (UDG), containing four molecules in the asymmetric unit, and two
forms of its complex with the proteinaceous inhibitor Ugi, containing two and
four crystallographically independent complexes, have been determined. A
comparison of these structures and the already known crystal structures
containing UDG shows that the enzyme can be considered to be made up of two
independently moving structural entities or domains. A detailed study of free
and DNA-bound human enzyme strengthens this conclusion. The domains close upon
binding to uracil-containing DNA, whereas they do not appear to do so upon
binding to Ugi. The comparative study also shows that the mobility of the
molecule involves the rigid-body movement of the domains superposed on
flexibility within domains.
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Figure 3.
Figure 3 Delineation of domains in EcUDG. Domain 1 is in green
and domain 2 is in red. The linker region is in purple. The axis
about which the domains move during closure is also shown.
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Figure 4.
Figure 4 Stereoview illustrating domain closure in EcUDG. Domain
1 of the free enzyme (dark) and that of the enzyme complexed
with single-stranded DNA (light) are superposed. The axis about
which the molecule has to rotate to bring domain 2 into
superposition is perpendicular to the figure and is indicated by
a ball.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2002,
58,
1269-1276)
copyright 2002.
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Secondary reference #1
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Title
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X-Ray analysis of a complex of escherichia coli uracil DNA glycosylase (ecudg) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic udg.
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Authors
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R.Ravishankar,
M.Bidya sagar,
S.Roy,
K.Purnapatre,
P.Handa,
U.Varshney,
M.Vijayan.
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Ref.
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Nucleic Acids Res, 1998,
26,
4880-4887.
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PubMed id
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Secondary reference #2
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Title
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Use of a coupled transcriptional system for consistent overexpression and purification of udg-Ugi complex and ugi from escherichia coli.
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Authors
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S.Roy,
K.Purnapatre,
P.Handa,
M.Boyanapalli,
U.Varshney.
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Ref.
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Protein Expr Purif, 1998,
13,
155-162.
[DOI no: ]
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PubMed id
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Secondary reference #3
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Title
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Protein mimicry of DNA from crystal structures of the uracil-Dna glycosylase inhibitor protein and its complex with escherichia coli uracil-Dna glycosylase.
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Authors
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C.D.Putnam,
M.J.Shroyer,
A.J.Lundquist,
C.D.Mol,
A.S.Arvai,
D.W.Mosbaugh,
J.A.Tainer.
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Ref.
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J Mol Biol, 1999,
287,
331-346.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. E. coli UDG: Ugi interface. (a) Stereo view of the
Ugi solvent-accessible surface at the hydrophobic pocket
(yellow) that binds the protruding E. coli UDG Leu191 side-chain
(blue). The Leu191 conformation is dictated by steric
interactions with Val43 and Met56. (b) Stereo view of the
interactions between the DNA binding residues of E. coli UDG
(green side-chains and grey C^α trace) and the Ugi β1 edge
(gold). As in human UDG:DNA complexes [Slupphaug et al 1996 and
Parikh et al 1998], this interface is fairly polar and hydrated
and contains all of the DNA-phosphate mimicking interactions of
Ugi. The uracil nucleotide recognition pocket is located beneath
the Ugi Ile22 side-chain.
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Figure 8.
Figure 8. β-Zipper conformational changes in UDG. β-Zipper
conformational change at the UDG topological switch point in the
open (blue) and closed (green) conformations. In the open
conformation observed in the E. coli UDG:Ugi complexes as well
as unbound and Ugi bound human [Mol et al 1995a and Mol et
al 1995b] and HSV [Savva et al 1995 and Savva and Pearl 1995b]
enzymes, UDG Leu61 in β1 is not within hydrogen bonding
distance of Leu162 and Trp164, and a water molecule is
coordinated between the strands (large red sphere). In the
closed conformation observed in human UDG:DNA complexes
[Slupphaug et al 1996 and Parikh et al 1998], the central
β-strands move together, extending the β-sheet connectivity
and displacing the central water molecule.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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