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PDBsum entry 1npy
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Structural genomics, unknown function
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PDB id
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1npy
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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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Crystal structure of a novel shikimate dehydrogenase from haemophilus influenzae.
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Authors
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S.Singh,
S.Korolev,
O.Koroleva,
T.Zarembinski,
F.Collart,
A.Joachimiak,
D.Christendat.
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Ref.
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J Biol Chem, 2005,
280,
17101-17108.
[DOI no: ]
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PubMed id
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Abstract
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To date two classes of shikimate dehydrogenases have been identified and
characterized, YdiB and AroE. YdiB is a bifunctional enzyme that catalyzes the
reversible reductions of dehydroquinate to quinate and dehydroshikimate to
shikimate in the presence of either NADH or NADPH. In contrast, AroE catalyzes
the reversible reduction of dehydroshikimate to shikimate in the presence of
NADPH. Here we report the crystal structure and biochemical characterization of
HI0607, a novel class of shikimate dehydrogenase annotated as shikimate
dehydrogenase-like. The kinetic properties of HI0607 are remarkably different
from those of AroE and YdiB. In comparison with YdiB, HI0607 catalyzes the
oxidation of shikimate but not quinate. The turnover rate for the oxidation of
shikimate is approximately 1000-fold lower compared with that of AroE.
Phylogenetic analysis reveals three independent clusters representing three
classes of shikimate dehydrogenases, namely AroE, YdiB, and this newly
characterized shikimate dehydrogenase-like protein. In addition, mutagenesis
studies of two invariant residues, Asp-103 and Lys-67, indicate that they are
important catalytic groups that may function as a catalytic pair in the
shikimate dehydrogenase reaction. This is the first study that describes the
crystal structure as well as mutagenesis and mechanistic analysis of this new
class of shikimate dehydrogenase.
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Figure 1.
FIG. 1. Bayesian-inferred, unrooted phylogeny of the
shikimate dehydrogenase family of enzymes. The radial tree,
produced by MRBAYES version 3.04b, clearly indicates three
distinct subgroups, which are AroE, YdiB, and SDH-L. Genetic
distances (calculated with MEGA2) between the classes are
calculated to be 1.89 (AroE-YdiB), 1.79 (SDH-L-YdiB), and 2.22
(SDH-L-AroE); genetic distances within each group are 0.468
(AroE), 0.601 (SDH-L), and 0.842 (YdiB). NCBI protein data base
accession numbers for the proteins of the SDH-L subgroup are as
follows: H. influenzae, ZP_00154645; Mannheimia
succiniciproducens, YP_089507; Pasteurella multocida, AAK03513
[GenBank]
Yersinia pestis, NP_405191 [GenBank]
; Salmonella typhimurium, NP_462758 [GenBank]
; Deinococcus radiodurans, NP_293803 [GenBank]
; Pseudomonas fluorescens, ZP_00263633; Pseudomonas putida,
AAN69362 [GenBank]
Corynebacterium efficiens, NP_737804 [GenBank]
; and Pseudomonas syringae, ZP_00123871. NCBI protein data base
accession numbers for the proteins of the YdiB subgroup are as
follows: E. coli, NP_310426 [GenBank]
; Shigella flexneri, NP_837377 [GenBank]
; S. typhimurium, NP_460325 [GenBank]
; Lactobacillus plantarum, NP_786702 [GenBank]
; Streptococcus pyognes, YP_060639; Enterococcus faecalis,
NP_815278 [GenBank]
; Enterococcus faecium, ZP_00285321; and Listeria monocytogenes,
ZP_00232331. NCBI protein data base accession numbers for the
proteins of the AroE subgroup are as follows: E. coli, NP_417740
[GenBank]
; S. flexneri, NP_709069 [GenBank]
; S. typhimurium, NP_462305 [GenBank]
; Y. pestis, NP_403898 [GenBank]
; Ewinia carotovora, YP_052082; and Photorhabdus luminescens,
CAE17063 [GenBank]
The branch confidence values are given as posterior
probabilities. The distance scale is shown at the bottom left.
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Figure 2.
FIG. 2. A, ribbon diagram of HI0607 monomer. The protein is
essentially composed of two distinct domains, a nucleotide
domain and a substrate-binding domain, which are linked by two
long helices, helices 4 and 9. B, the biological dimer of
HI0607. Dimerization is mediated via hydrophobic interactions
between the N-terminal  2 and  1
structures of each monomer. C, HI0607 active site. In addition
to the two ionizable groups, Lys-67 and Asp-103, there are a
number of polar groups in the active site (Gln-242, Asn-88, and
Asn-101). Toward the back of the pocket one encounters a cluster
of serines (Ser-11, Ser-13, Ser-17, and Ser-63), Thr-89, and
other polar groups including tyrosines (Tyr-37, for example).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2005,
280,
17101-17108)
copyright 2005.
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