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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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Atomic resolution structure of erwinia chrysanthemi l-asparaginase
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Structure:
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L-asparaginase. Chain: a, b, c, d. Synonym: l-asparagine amidohydrolase, l-asnase. Ec: 3.5.1.1
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Source:
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Erwinia chrysanthemi. Organism_taxid: 556
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Biol. unit:
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Tetramer (from PDB file)
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Resolution:
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1.0Å
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R-factor:
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0.109
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R-free:
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0.128
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Authors:
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J.Lubkowski,M.Dauter,K.Aghaiypour,A.Wlodawer,Z.Dauter
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Key ref:
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J.Lubkowski
et al.
(2003).
Atomic resolution structure of Erwinia chrysanthemi L-asparaginase.
Acta Crystallogr D Biol Crystallogr,
59,
84-92.
PubMed id:
DOI:
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Date:
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07-Nov-02
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Release date:
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04-Dec-02
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PROCHECK
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Headers
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References
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P06608
(ASPG_ERWCH) -
L-asparaginase
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Seq: Struc:
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348 a.a.
325 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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Enzyme class:
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E.C.3.5.1.1
- Asparaginase.
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Reaction:
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L-asparagine + H2O = L-aspartate + NH3
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L-asparagine
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+
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H(2)O
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=
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L-aspartate
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+
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NH(3)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Biological process
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cellular amino acid metabolic process
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2 terms
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Biochemical function
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hydrolase activity
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2 terms
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DOI no:
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Acta Crystallogr D Biol Crystallogr
59:84-92
(2003)
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PubMed id:
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Atomic resolution structure of Erwinia chrysanthemi L-asparaginase.
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J.Lubkowski,
M.Dauter,
K.Aghaiypour,
A.Wlodawer,
Z.Dauter.
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ABSTRACT
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An X-ray structure of L-asparaginase from Erwinia chrysanthemi (ErA) has been
refined at 1 A resolution to an R factor of below 0.1, using data collected on a
synchrotron source. With four molecules of the enzyme consisting of 327 amino
acids each, this crystal contains one of the largest asymmetric units of a
protein refined to date at atomic resolution. Previously, structures of ErA and
of related enzymes from other bacterial sources have been refined at resolutions
not exceeding 1.7 A; thus, the present structure represents a very significant
improvement in the quality of the available models of these proteins and should
provide a good basis for future studies of the conformational variability of
proteins, identification of subtle conformational features and corroboration of
the stereochemical libraries, amongst other things. L-Asparaginases, which are
enzymes that catalyze the hydrolysis of L-asparagine to aspartic acid, have been
used for over 30 y as therapeutic agents in the treatment of acute childhood
lymphoblastic leukemia, although the details of the enzymatic reaction and
substrate specificity have not yet been completely elucidated. This atomic
resolution structure is a step in that direction.
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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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L.Gabison,
M.Chiadmi,
M.El Hajji,
B.Castro,
N.Colloc'h,
and
T.Prangé
(2010).
Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand.
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Acta Crystallogr D Biol Crystallogr, 66,
714-724.
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PDB codes:
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P.Dhavala,
J.Krasotkina,
C.Dubreuil,
and
A.C.Papageorgiou
(2008).
Expression, purification and crystallization of Helicobacter pylori L-asparaginase.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 64,
740-742.
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M.K.Yun,
A.Nourse,
S.W.White,
C.O.Rock,
and
R.J.Heath
(2007).
Crystal structure and allosteric regulation of the cytoplasmic Escherichia coli L-asparaginase I.
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J Mol Biol, 369,
794-811.
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PDB codes:
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A.Gutteridge,
and
J.M.Thornton
(2005).
Understanding nature's catalytic toolkit.
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Trends Biochem Sci, 30,
622-629.
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L.E.Wikman,
J.Krasotkina,
A.Kuchumova,
N.N.Sokolov,
and
A.C.Papageorgiou
(2005).
Crystallization and preliminary crystallographic analysis of L-asparaginase from Erwinia carotovora.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 61,
407-409.
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D.Borek,
K.Michalska,
K.Brzezinski,
A.Kisiel,
J.Podkowinski,
D.T.Bonthron,
D.Krowarsch,
J.Otlewski,
and
M.Jaskolski
(2004).
Expression, purification and catalytic activity of Lupinus luteus asparagine beta-amidohydrolase and its Escherichia coli homolog.
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Eur J Biochem, 271,
3215-3226.
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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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