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PDBsum entry 1b54
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Hypothetical protein
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PDB id
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1b54
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References listed in PDB file
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Key reference
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Title
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Structure of a yeast hypothetical protein selected by a structural genomics approach.
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Authors
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S.Eswaramoorthy,
S.Gerchman,
V.Graziano,
H.Kycia,
F.W.Studier,
S.Swaminathan.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2003,
59,
127-135.
[DOI no: ]
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PubMed id
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Abstract
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Yeast hypothetical protein YBL036C (SWISS-PROT P38197), initially thought to be
a member of an 11-protein family, was selected for crystal structure
determination since no structural or functional information was available. The
structure has been determined independently by MIR and MAD methods to 2.0 A
resolution. The MAD structure was determined largely through automated model
building. The protein folds as a TIM barrel beginning with a long N-terminal
helix, in contrast to the classic triose phosphate isomerase (TIM) structure,
which begins with a beta-strand. A cofactor, pyridoxal 5'-phosphate, is
covalently bound near the C-terminal end of the barrel, the usual active site in
TIM-barrel folds. A single-domain monomeric molecule, this yeast protein
resembles the N-terminal domain of alanine racemase or ornithine decarboxylase,
both of which are two-domain dimeric proteins. The yeast protein has been shown
to have amino-acid racemase activity. Although selected as a member of a protein
family having no obvious relationship to proteins of known structure, the
protein fold turned out to be a well known and widely distributed fold. This
points to the need for a more comprehensive base of structural information and
better structure-modeling tools before the goal of structure prediction from
amino-acid sequences can be realised. In this case, similarity to a known
structure allowed inferences to be made about the structure and function of a
widely distributed protein family.
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Figure 3.
Figure 3 (a) A schematic diagram with the numbering scheme of
PLP. (b) Stereoview of the active site of the yeast protein
P007. The cofactor and residues involved in the active site are
shown as a ball-and-stick model along with the C^  trace
of the protein. The cofactor PLP is covalently bound to Lys49
and makes a hydrogen bond with Arg239. The phosphate group
interacts with Ser224 and Thr242. The O3 of the pyridine ring
makes a hydrogen bond to Asp70.
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Figure 4.
Figure 4 Superposition of P007 and the TIM-barrel domain of ARC
shows similarity near the active site. The helices and the
strands at the other side deviate considerably. The brute-force
alignment of LSQMAN matched 154 atoms with an r.m.s.d. of 1.72
Å.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2003,
59,
127-135)
copyright 2003.
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