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PDBsum entry 1mbt
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Oxidoreductase
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PDB id
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1mbt
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References listed in PDB file
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Key reference
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Title
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The structure of the substrate-Free form of murb, An essential enzyme for the synthesis of bacterial cell walls.
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Authors
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T.E.Benson,
C.T.Walsh,
J.M.Hogle.
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Ref.
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Structure, 1996,
4,
47-54.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: The repeating disaccharide and pentapeptide units of the bacterial
peptidoglycan layer are connected by a lactyl ether bridge biosynthesized from
UDP-N-acetylglucosamine and phosphoenolpyruvate in sequential enol ether
transfer and reduction steps catalyzed by MurA and MurB respectively. Knowledge
of the structure and mechanism of the MurB enzyme will permit analysis of this
unusual enol ether reduction reaction and may facilitate the design of
inhibitors as candidate next-generation antimicrobial agents. RESULTS: The
crystal structure of UDP-N-acetylenolpyruvylglucosamine reductase, MurB, has
been solved at 3.0 A and compared with our previously reported structure of MurB
complexed with its substrate enolpyruvyl-UDP-N- acetylglucosamine. Comparison of
the liganded structure of MurB with this unliganded form reveals that the
binding of substrate induces a substantial movement of domain 3 (residues
219-319) of the enzyme and a significant rearrangement of a loop within this
domain. These ligand induced changes disrupt a stacking interaction between two
tyrosines (Tyr190 and Tyr254) which lie at the side of the channel leading to
the active site of the free enzyme. CONCLUSIONS: The conformational change
induced by enolpyruvyl-UDP-N- acetylglucosamine binding to MurB results in the
closure of the substrate-binding channel over the substrate. Tyr190 swings over
the channel opening and establishes a hydrogen bond with an oxygen of the
alpha-phosphate of the sugar nucleotide substrate which is critical to substrate
binding.
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Figure 1.
Figure 1. Proposed mechanism of reduction of the enolpyruvyl
group of EP-UDP-GlcNAc by MurB [3 and 5]. Hydride transfer to C3
is proposed to generate a carbanion equivalent that can be
stabilized by protonation from Glu325 and/or Arg159. Quenching
of the carbanion is proposed to be mediated by Ser229. Figure
1. Proposed mechanism of reduction of the enolpyruvyl group
of EP-UDP-GlcNAc by MurB [[3]3 and [4]5]. Hydride transfer to C3
is proposed to generate a carbanion equivalent that can be
stabilized by protonation from Glu325 and/or Arg159. Quenching
of the carbanion is proposed to be mediated by Ser229.
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Figure 5.
Figure 5. Surface representations of the substrate-free and
EP-UDP-GlcNAc-bound MurB structures. (a) Molecular and charge
surfaces of the substrate-free MurB with a view of the uracil
portion of the bound flavin. This representation shows access to
the flavin and the charge distribution at the channel
(positively charged areas shown in blue, negatively charged
areas shown in red, and neutral areas shown in white). (b) The
EP-UDP-GlcNAc–MurB complex. The substrate-bound MurB shows
structural and charge-distribution changes induced upon
substrate binding. Figure 5. Surface representations of the
substrate-free and EP-UDP-GlcNAc-bound MurB structures. (a)
Molecular and charge surfaces of the substrate-free MurB with a
view of the uracil portion of the bound flavin. This
representation shows access to the flavin and the charge
distribution at the channel (positively charged areas shown in
blue, negatively charged areas shown in red, and neutral areas
shown in white). (b) The EP-UDP-GlcNAc–MurB complex. The
substrate-bound MurB shows structural and charge-distribution
changes induced upon substrate binding. (Figure generated using
GRASP [[4]27].)
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The above figures are
reprinted
by permission from Cell Press:
Structure
(1996,
4,
47-54)
copyright 1996.
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Secondary reference #1
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Title
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An enzyme-Substrate complex involved in bacterial cell wall biosynthesis.
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Authors
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T.E.Benson,
D.J.Filman,
C.T.Walsh,
J.M.Hogle.
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Ref.
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Nat Struct Biol, 1995,
2,
644-653.
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PubMed id
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Secondary reference #2
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Title
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Crystallization and preliminary X-Ray crystallographic studies of udp-N-Acetylenolpyruvylglucosamine reductase.
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Authors
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T.E.Benson,
C.T.Walsh,
J.M.Hogle.
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Ref.
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Protein Sci, 1994,
3,
1125-1127.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1: A: Crystals of MurBin the presence of UDPGlcNAcEP. B: Methyl mercury nitrate derivative difference Patterson,
12-3 A, w section 0.5, contoured at lo starting at lo above the mean density.This peakis consistent with a heavy atom
atposition x = 0.063, y 0.164, 5 = 0.287. The X's mark the positions of the calculated Patterson peaks based on this site.
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The above figure is
reproduced from the cited reference
which is an Open Access publication published by the Protein Society
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Secondary reference #3
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Title
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Overexpression, Purification, And mechanistic study of udp-N-Acetylenolpyruvylglucosamine reductase.
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Authors
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T.E.Benson,
J.L.Marquardt,
A.C.Marquardt,
F.A.Etzkorn,
C.T.Walsh.
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Ref.
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Biochemistry, 1993,
32,
2024-2030.
[DOI no: ]
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PubMed id
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