1MBB

OXIDOREDUCTASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

(E)-enolbutyryl-UDP-N-acetylglucosamine as a mechanistic probe of UDP-N-acetylenolpyruvylglucosamine reductase (MurB).

Lees, W.J.Benson, T.E.Hogle, J.M.Walsh, C.T.

(1996) Biochemistry 35: 1342-1351

  • DOI: 10.1021/bi952287w
  • Primary Citation of Related Structures:  
    1MBB

  • PubMed Abstract: 
  • UDP-N-acetylenolpyruvylglucosamine reductase (MurB), a peptidoglycan biosynthetic enzyme from Escherichia coli, reduces both (E)- and (Z)-isomers of enolbutyryl-UDP-GlcNAc, C4 analogs of the physiological C3 enolpyruvyl substrate, to UDP-methyl-N-acetylmuramic acid in the presence of NADPH ...

    UDP-N-acetylenolpyruvylglucosamine reductase (MurB), a peptidoglycan biosynthetic enzyme from Escherichia coli, reduces both (E)- and (Z)-isomers of enolbutyryl-UDP-GlcNAc, C4 analogs of the physiological C3 enolpyruvyl substrate, to UDP-methyl-N-acetylmuramic acid in the presence of NADPH. The X-ray crystal structure of the (E)-enolbutyryl-UDP-GlcNAc-MurB complex is similar to that of the enolpyruvyl-UDP-GlcNAc-MurB complex. In both structures the groups thought to be involved in hydride transfer to C3 and protonation at C2 of the enol ether substrate are arranged anti relative to the enol double bond. The stereochemical outcome of reduction of (E)-enolbutyryl-UDP-GlcNAc by NADPD in D2O is thus predicted to yield a (2R,3R)-dideuterio product. This was validated by conversion of the 2,3-dideuterio-UDP-methyl-N-acetylmuramic acid product to 2,3-dideuterio-2-hydroxybutyrate, which was shown to be (2R) by enzymatic analysis and (3R) by NMR comparison to authentic (2R,3R)- and (2R,3S)-2,3-dideuterio-2-hydroxybutyrate. Remarkably, the (E)-enolbutyryl-UDP-GlcNAc was found to partition between reduction to UDP-methyl-N-acetylmuramic and isomerization to the (Z)-substrate isomer in the MurB active site, indicative of a C2 carbanion/enol species that is sufficiently long-lived to rotate around the C2-C3 single bond during catalysis.


    Related Citations: 
    • An Enzyme-Substrate Complex Involved in Bacterial Cell Wall Biosynthesis
      Benson, T.E., Filman, D.J., Walsh, C.T., Hogle, J.M.
      (1995) Nat Struct Biol 2: 644
    • Crystallization and Preliminary X-Ray Crystallographic Studies of Udp-N-Acetyl Enolpyruvylglucosamine Reductase
      Benson, T.E., Walsh, C.T., Hogle, J.M.
      (1994) Protein Sci 3: 1125
    • Overexpression, Purification, and Mechanistic Study of Udp-N-Acetylenolpyruvylglucosamine Reductase
      Benson, T.E., Marquardt, J.L., Marquardt, A.C., Etzkorn, F.A., Walsh, C.T.
      (1993) Biochemistry 32: 2024

    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
URIDINE DIPHOSPHO-N-ACETYLENOLPYRUVYLGLUCOSAMINE REDUCTASEA342Escherichia coliMutation(s): 0 
EC: 1.1.1.158 (PDB Primary Data), 1.3.1.98 (UniProt)
Find proteins for P08373 (Escherichia coli (strain K12))
Explore P08373 
Go to UniProtKB:  P08373
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
EEB
Query on EEB

Download Ideal Coordinates CCD File 
B [auth A]URIDINE-DIPHOSPHATE-3(N-ACETYLGLUCOSAMINYL)BUTYRIC ACID
C21 H33 N3 O19 P2
DFCARJAECCPPGB-LHYXAPFASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50α = 90
b = 50β = 90
c = 264.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance