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* Residue conservation analysis
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PDB id:
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Lyase
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Title:
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The x-ray crystal structure of the paramecium bursaria chlorella virus arginine decarboxylase bound to agmatine
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Structure:
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Arginine decarboxylase, a207r protein. Chain: a, b, c, d, e, f, g, h. Engineered: yes
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Source:
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Paramecium bursaria chlorella virus 1. Organism_taxid: 10506. Gene: a207r. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Resolution:
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1.80Å
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R-factor:
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0.219
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R-free:
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0.238
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Authors:
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R.H.Shah,R.Akella,E.Goldsmith,M.A.Phillips
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Key ref:
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R.Shah
et al.
(2007).
X-ray structure of Paramecium bursaria Chlorella virus arginine decarboxylase: insight into the structural basis for substrate specificity.
Biochemistry,
46,
2831-2841.
PubMed id:
DOI:
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Date:
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11-Nov-06
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Release date:
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20-Mar-07
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PROCHECK
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Headers
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References
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Q84527
(Q84527_PBCV1) -
Arginine/Ornithine decarboxylase
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Seq:
Struc:
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372 a.a.
369 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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Gene Ontology (GO) functional annotation
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Biological process
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polyamine biosynthetic process
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1 term
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Biochemical function
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catalytic activity
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1 term
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DOI no:
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Biochemistry
46:2831-2841
(2007)
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PubMed id:
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X-ray structure of Paramecium bursaria Chlorella virus arginine decarboxylase: insight into the structural basis for substrate specificity.
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R.Shah,
R.Akella,
E.J.Goldsmith,
M.A.Phillips.
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ABSTRACT
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The group IV pyridoxal-5'-phosphate (PLP)-dependent decarboxylases belong to the
beta/alpha barrel structural family, and include enzymes with substrate
specificity for a range of basic amino acids. A unique homolog of this family,
the Paramecium bursaria Chlorella virus arginine decarboxylase (cvADC), shares
about 40% amino acid sequence identity with the eukaryotic ornithine
decarboxylases (ODCs). The X-ray structure of cvADC has been solved to 1.95 and
1.8 A resolution for the free and agmatine (product)-bound enzymes. The global
structural differences between cvADC and eukaryotic ODC are minimal (rmsd of
1.2-1.4 A); however, the active site has significant structural rearrangements.
The key "specificity element," is identified as the 310-helix that
contains and positions substrate-binding residues such as E296 cvADC (D332 in T.
brucei ODC). In comparison to the ODC structures, the 310-helix in cvADC is
shifted over 2 A away from the PLP cofactor, thus accommodating the larger
arginine substrate. Within the context of this conserved fold, the protein is
designed to be flexible in the positioning and amino acid sequence of the
310-helix, providing a mechanism to evolve different substrate preferences
within the family without large structural rearrangements. Also, in the
structure, the "K148-loop" (homologous to the "K169-loop" of
ODC) is observed in a closed, substrate-bound conformation for the first time.
Apparently the K148 loop is a mobile loop, analogous to those observed in triose
phosphate isomerase and tryptophan synthetase. In conjunction with prior
structural studies these data predict that this loop adopts different
conformations throughout the catalytic cycle, and that loop movement may be
kinetically linked to the rate-limiting step of product release.
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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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S.Weyand,
G.Kefala,
D.I.Svergun,
and
M.S.Weiss
(2009).
The three-dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation.
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J Struct Funct Genomics, 10,
209-217.
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PDB code:
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X.Y.Liu,
J.Lei,
X.Liu,
X.D.Su,
and
L.Li
(2009).
Preliminary X-ray crystallographic studies of Bacillus subtilis SpeA protein.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 65,
282-284.
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T.Hu,
D.Wu,
J.Chen,
J.Ding,
H.Jiang,
and
X.Shen
(2008).
The catalytic intermediate stabilized by a "down" active site loop for diaminopimelate decarboxylase from Helicobacter pylori. Enzymatic characterization with crystal structure analysis.
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J Biol Chem, 283,
21284-21293.
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E.K.Willert,
R.Fitzpatrick,
and
M.A.Phillips
(2007).
Allosteric regulation of an essential trypanosome polyamine biosynthetic enzyme by a catalytically dead homolog.
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Proc Natl Acad Sci U S A, 104,
8275-8280.
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J.Lee,
A.J.Michael,
D.Martynowski,
E.J.Goldsmith,
and
M.A.Phillips
(2007).
Phylogenetic diversity and the structural basis of substrate specificity in the beta/alpha-barrel fold basic amino acid decarboxylases.
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J Biol Chem, 282,
27115-27125.
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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
code is
shown on the right.
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Links
