1RYW

C115S MurA liganded with reaction products


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Evidence That the Fosfomycin Target Cys115 in UDP-N-acetylglucosamine Enolpyruvyl Transferase (MurA) Is Essential for Product Release.

Eschenburg, S.Priestman, M.Schonbrunn, E.

(2005) J Biol Chem 280: 3757-3763

  • DOI: 10.1074/jbc.M411325200
  • Primary Citation of Related Structures:  
    1RYW

  • PubMed Abstract: 
  • MurA (UDP-N-acetylglucosamine enolpyruvyl transferase, EC 2.5.1.7) is an essential enzyme in the biosynthesis of the peptidoglycan layer of the bacterial cell. It provides an attractive template for the design of novel antibiotic drugs and is the target of the naturally occurring antibiotic fosfomycin, which covalently attaches to Cys115 in the active site of the enzyme ...

    MurA (UDP-N-acetylglucosamine enolpyruvyl transferase, EC 2.5.1.7) is an essential enzyme in the biosynthesis of the peptidoglycan layer of the bacterial cell. It provides an attractive template for the design of novel antibiotic drugs and is the target of the naturally occurring antibiotic fosfomycin, which covalently attaches to Cys115 in the active site of the enzyme. Mutations of Cys115 to Asp exist in pathogens such as Mycobacteria or Chlamydia rendering these organisms resistant to fosfomycin. Thus, there is a need for the elucidation of the role of this cysteine in the MurA reaction. We determined the x-ray structure of the C115S mutant of Enterobacter cloacae MurA, which was crystallized in the presence of the substrates of MurA. The structure depicts the product state of the enzyme with enolpyruvyl-UDP-N-acetylglucosamine and inorganic phosphate trapped in the active site. Kinetic analysis revealed that the Cys-to-Ser mutation results in an enzyme that appears to perform a single turnover of the reaction. Opposing the common view of Cys115 as a key residue in the chemical reaction of enolpyruvyl transfer, we now conclude that the wild-type cysteine is essential for product release only. On the basis of a detailed comparison of the product state with the intermediate state and an unliganded state of MurA, we propose that dissociation of the products is an ordered event with inorganic phosphate leaving first. Phosphate departure appears to trigger a suite of conformational changes, which finally leads to opening of the two-domain structure of MurA and the release of the second product enolpyruvyl-UDP-N-acetylglucosamine.


    Organizational Affiliation

    Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66045, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine 1-carboxyvinyltransferase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
419Enterobacter cloacaeMutation(s): 2 
Gene Names: murAmurZ
EC: 2.5.1.7
UniProt
Find proteins for P33038 (Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCTC 10005 / WDCM 00083 / NCDC 279-56))
Explore P33038 
Go to UniProtKB:  P33038
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33038
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPU
Query on EPU

Download Ideal Coordinates CCD File 
CA [auth E],
GA [auth F],
J [auth A],
KA [auth G],
N [auth B],
CA [auth E],
GA [auth F],
J [auth A],
KA [auth G],
N [auth B],
NA [auth H],
R [auth C],
Y [auth D]
URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID
C20 H29 N3 O19 P2
BEGZZYPUNCJHKP-DBYWSUQTSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
BA [auth E],
FA [auth F],
I [auth A],
IA [auth G],
JA [auth G],
BA [auth E],
FA [auth F],
I [auth A],
IA [auth G],
JA [auth G],
M [auth B],
MA [auth H],
Q [auth C],
X [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D],
DA [auth E],
EA [auth E],
HA [auth F],
K [auth A],
AA [auth D],
DA [auth E],
EA [auth E],
HA [auth F],
K [auth A],
L [auth A],
LA [auth G],
O [auth B],
OA [auth H],
P [auth B],
PA [auth H],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.867α = 90
b = 153.729β = 104.17
c = 135.089γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Database references, Derived calculations, Non-polymer description
  • Version 1.4: 2021-10-27
    Changes: Advisory, Database references, Derived calculations