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PDBsum entry 1rcq
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Contents |
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* Residue conservation analysis
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PDB id:
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Isomerase
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Title:
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The 1.45 a crystal structure of alanine racemase from a pathogenic bacterium, pseudomonas aeruginosa, contains both internal and external aldimine forms
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Structure:
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Catabolic alanine racemase dadx. Chain: a. Engineered: yes
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Source:
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Pseudomonas aeruginosa. Organism_taxid: 287. Gene: dadx. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
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Biol. unit:
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Dimer (from PDB file)
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Resolution:
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1.45Å
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R-factor:
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0.153
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R-free:
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0.206
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Authors:
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P.Le Magueres,H.Im,A.Dvorak,U.Strych,M.Benedik,K.L.Krause
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Key ref:
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P.LeMagueres
et al.
(2003).
Crystal structure at 1.45 A resolution of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms.
Biochemistry,
42,
14752-14761.
PubMed id:
DOI:
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Date:
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04-Nov-03
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Release date:
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01-Jun-04
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PROCHECK
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Headers
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References
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Q9HTQ2
(ALR2_PSEAE) -
Alanine racemase, catabolic from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
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Seq:
Struc:
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357 a.a.
357 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.5.1.1.1
- alanine racemase.
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Reaction:
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L-alanine = D-alanine
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L-alanine
Bound ligand (Het Group name = )
matches with 60.00% similarity
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=
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D-alanine
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Cofactor:
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Pyridoxal 5'-phosphate
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Pyridoxal 5'-phosphate
Bound ligand (Het Group name =
PLP)
matches with 93.75% similarity
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Biochemistry
42:14752-14761
(2003)
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PubMed id:
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Crystal structure at 1.45 A resolution of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms.
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P.LeMagueres,
H.Im,
A.Dvorak,
U.Strych,
M.Benedik,
K.L.Krause.
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ABSTRACT
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The structure of the catabolic alanine racemase, DadX, from the pathogenic
bacterium Pseudomonas aeruginosa, reported here at 1.45 A resolution, is a dimer
in which each monomer is comprised of two domains, an eight-stranded alpha/beta
barrel containing the PLP cofactor and a second domain primarily composed of
beta-strands. The geometry of each domain is very similar to that of Bacillus
stearothermophilus alanine racemase, but the rotation between domains differs by
about 15 degrees. This change does not alter the structure of the active site in
which almost all residues superimpose well with a low rms difference of 0.86 A.
Unexpectedly, the active site of DadX contains a guest substrate that is located
where acetate and propionate have been observed in the Bacillus structures. It
is modeled as d-lysine and oriented such that its terminal NZ atom makes a
covalent bond with C4' of PLP. Since the internal aldimine bond between the
protein lysine, Lys33, and C4' of PLP is also unambiguously observed, there
appears to be an equilibrium between both internally and externally reacted
forms. The PLP cofactor adopts two partially occupied conformational states that
resemble previously reported internal and external aldimine complexes.
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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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E.R.Scaletti,
S.R.Luckner,
and
K.L.Krause
(2012).
Structural features and kinetic characterization of alanine racemase from Staphylococcus aureus (Mu50).
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Acta Crystallogr D Biol Crystallogr,
68,
82-92.
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PDB code:
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J.Ju,
S.Xu,
Y.Furukawa,
Y.Zhang,
H.Misono,
T.Minamino,
K.Namba,
B.Zhao,
and
K.Ohnishi
(2011).
Correlation between catalytic activity and monomer-dimer equilibrium of bacterial alanine racemases.
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J Biochem,
149,
83-89.
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C.Bakolitsa,
A.Kumar,
D.McMullan,
S.S.Krishna,
M.D.Miller,
D.Carlton,
R.Najmanovich,
P.Abdubek,
T.Astakhova,
H.J.Chiu,
T.Clayton,
M.C.Deller,
L.Duan,
Y.Elias,
J.Feuerhelm,
J.C.Grant,
S.K.Grzechnik,
G.W.Han,
L.Jaroszewski,
K.K.Jin,
H.E.Klock,
M.W.Knuth,
P.Kozbial,
D.Marciano,
A.T.Morse,
E.Nigoghossian,
L.Okach,
S.Oommachen,
J.Paulsen,
R.Reyes,
C.L.Rife,
C.V.Trout,
H.van den Bedem,
D.Weekes,
A.White,
Q.Xu,
K.O.Hodgson,
J.Wooley,
M.A.Elsliger,
A.M.Deacon,
A.Godzik,
S.A.Lesley,
and
I.A.Wilson
(2010).
The structure of the first representative of Pfam family PF06475 reveals a new fold with possible involvement in glycolipid metabolism.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
66,
1211-1217.
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PDB code:
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R.M.Couñago,
M.Davlieva,
U.Strych,
R.E.Hill,
and
K.L.Krause
(2009).
Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames).
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BMC Struct Biol,
9,
53.
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PDB code:
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D.Wu,
T.Hu,
L.Zhang,
J.Chen,
J.Du,
J.Ding,
H.Jiang,
and
X.Shen
(2008).
Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis.
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Protein Sci,
17,
1066-1076.
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PDB codes:
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K.Kino,
M.Sato,
M.Yoneyama,
and
K.Kirimura
(2007).
Synthesis of DL-tryptophan by modified broad specificity amino acid racemase from Pseudomonas putida IFO 12996.
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Appl Microbiol Biotechnol,
73,
1299-1305.
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U.Strych,
M.Davlieva,
J.P.Longtin,
E.L.Murphy,
H.Im,
M.J.Benedik,
and
K.L.Krause
(2007).
Purification and preliminary crystallization of alanine racemase from Streptococcus pneumoniae.
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BMC Microbiol,
7,
40.
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J.Ju,
K.Yokoigawa,
H.Misono,
and
K.Ohnishi
(2005).
Cloning of alanine racemase genes from Pseudomonas fluorescens strains and oligomerization states of gene products expressed in Escherichia coli.
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J Biosci Bioeng,
100,
409-417.
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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
