1UXY

MURB MUTANT WITH SER 229 REPLACED BY ALA, COMPLEX WITH ENOLPYRUVYL-UDP-N-ACETYLGLUCOSAMINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-ray crystal structures of the S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine at 1.8-A resolution.

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

(1997) Biochemistry 36: 806-811

  • DOI: 10.1021/bi962221g
  • Primary Citation of Related Structures:  
    1UXY, 2MBR

  • PubMed Abstract: 
  • MurB catalyzes the second committed step in the synthesis of peptidoglycan, a key component of the bacterial cell wall. The crystal structures of both a S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine were solved and refined at 1 ...

    MurB catalyzes the second committed step in the synthesis of peptidoglycan, a key component of the bacterial cell wall. The crystal structures of both a S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine were solved and refined at 1.8 A resolution. The single point mutation of residue 229 from serine to alanine eliminated a hydroxyl group which has previously been proposed to play a critical role as a proton donor during the second half-reaction of MurB, namely, reoxidation of FADH2 and reduction of the enolpyruvyl substrate. The mutation also resulted in the loss of the water molecule-hydrogen bonded to the serine hydroxyl in the wild-type structure changing the hydrogen-bonding network with in the active site. Comparison of the wild-type and S229A mutant structures confirms that the dramatic kinetic defect of an approximately 10(7)-fold decrease observed for the Ser 229 Ala mutant in the second half-reaction [Benson, T.E., Walsh, C.T., & Massey, V. (1997) Biochemistry 36, 796-805] is a direct result of the loss of the serine hydroxyl moiety rather than other nonspecific active-site changes or general structural defects.


    Related Citations: 
    • Kinetic Characterization of Wild-Type and S229A Mutant Murb: Evidence for the Role of Ser 229 as a General Acid
      Benson, T.E., Walsh, C.T., Massey, V.
      (1997) Biochemistry 36: 796
    • 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) Int Immunol 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 REDUCTASEA340Escherichia coliMutation(s): 1 
EC: 1.1.1.158 (PDB Primary Data), 1.3.1.98 (UniProt)
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 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
EPU
Query on EPU

Download Ideal Coordinates CCD File 
C [auth A]URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID
C20 H29 N3 O19 P2
BEGZZYPUNCJHKP-DBYWSUQTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.2α = 90
b = 49.2β = 90
c = 261.8γ = 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: 1997-04-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance