3ISS

Crystal structure of enolpyruvyl-UDP-GlcNAc synthase (MurA):UDP-N-acetylmuramic acid:phosphite from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evidence of Kinetic Control of Ligand Binding and Staged Product Release in MurA (Enolpyruvyl UDP-GlcNAc Synthase)-Catalyzed Reactions .

Jackson, S.G.Zhang, F.Chindemi, P.Junop, M.S.Berti, P.J.

(2009) Biochemistry 48: 11715-11723

  • DOI: 10.1021/bi901524q
  • Also Cited By: 3SWD

  • PubMed Abstract: 
  • MurA (enolpyruvyl UDP-GlcNAc synthase) catalyzes the first committed step in peptidoglycan biosynthesis. In this study, MurA-catalyzed breakdown of its tetrahedral intermediate (THI), with a k(cat)/K(M) of 520 M(-1) s(-1), was far slower than the nor ...

    MurA (enolpyruvyl UDP-GlcNAc synthase) catalyzes the first committed step in peptidoglycan biosynthesis. In this study, MurA-catalyzed breakdown of its tetrahedral intermediate (THI), with a k(cat)/K(M) of 520 M(-1) s(-1), was far slower than the normal reaction, and 3 x 10(5)-fold slower than the homologous enzyme, AroA, reacting with its THI. This provided kinetic evidence of slow binding and a conformationally constrained active site. The MurA cocrystal structure with UDP-N-acetylmuramic acid (UDP-MurNAc), a potent inhibitor, and phosphite revealed a new "staged" MurA conformation in which the Arg397 side chain tracked phosphite out of the catalytic site. The closed-to-staged transition involved breaking eight MurA.ligand ion pairs, and three intraprotein hydrogen bonds helping hold the active site loop closed. These were replaced with only two MurA.UDP-MurNAc ion pairs, two with phosphite, and seven new intraprotein ion pairs or hydrogen bonds. Cys115 appears to have an important role in forming the staged conformation. The staged conformation appears to be one step in a complex choreography of release of the product from MurA.


    Organizational Affiliation

    Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton,Ontario L8S 4M1, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-acetylglucosamine 1-carboxyvinyltransferase
A, B, C, D, E, F, G, H, I, J, K, L
418Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: murA (murZ)
EC: 2.5.1.7
Find proteins for P0A749 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A749
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPU
Query on EPU

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID
ENOLPYRUVYL-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
C20 H29 N3 O19 P2
BEGZZYPUNCJHKP-DBYWSUQTSA-N
 Ligand Interaction
PO3
Query on PO3

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
PHOSPHITE ION
O3 P
AQSJGOWTSHOLKH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EPUKi: 900 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 84.510α = 111.52
b = 120.910β = 104.44
c = 139.730γ = 90.19
Software Package:
Software NamePurpose
ADSCdata collection
d*TREKdata reduction
PHASERphasing
PHENIXrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-07-27
    Type: Database references, Derived calculations, Non-polymer description