3KQA

MurA dead-end complex with terreic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

The fungal product terreic acid is a covalent inhibitor of the bacterial cell wall biosynthetic enzyme UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA) .

Han, H.Yang, Y.Olesen, S.H.Becker, A.Betzi, S.Schonbrunn, E.

(2010) Biochemistry 49: 4276-4282

  • DOI: https://doi.org/10.1021/bi100365b
  • Primary Citation of Related Structures:  
    3KQA, 3KR6, 3LTH

  • PubMed Abstract: 

    Terreic acid is a metabolite with antibiotic properties produced by the fungus Aspergillus terreus. We found that terreic acid is a covalent inhibitor of the bacterial cell wall biosynthetic enzyme MurA from Enterobacter cloacae and Escherichia coli in vitro. The crystal structure of the MurA dead-end complex with terreic acid revealed that the quinine ring is covalently attached to the thiol group of Cys115, the molecular target of the antibiotic fosfomycin. Kinetic characterization established that the inactivation requires the presence of substrate UNAG (UDP-N-acetylglucosamine), proceeding with an inactivation rate constant k(inact) of 130 M(-1) s(-1). Although the mechanisms of inactivation are similar, fosfomycin is approximately 50 times more potent than terreic acid, and the structural consequences of covalent modification by these two inhibitors are fundamentally different. The MurA-fosfomycin complex exists in the closed enzyme conformation, with the Cys115-fosfomycin adduct buried in the active site. In contrast, the dead-end complex with terreic acid is open, is free of UNAG, and has the Cys115-terreic acid adduct solvent-exposed. It appears that terreic acid reacts with Cys115 in the closed, binary state of the enzyme, but that the resulting Cys115-terreic acid adduct imposes steric clashes in the active site. As a consequence, the loop containing Cys115 rearranges, the enzyme opens, and UNAG is released. The differential kinetic and structural characteristics of MurA inactivation by terreic acid and fosfomycin reflect the importance of noncovalent binding potential, even for covalent inhibitors, in ensuring inactivation efficiency and specificity.


  • Organizational Affiliation

    Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine 1-carboxyvinyltransferase
A, B, C, D
419Enterobacter cloacaeMutation(s): 0 
Gene Names: murAMurA (MurZ)murZ
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TR9
Query on TR9

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
O [auth C],
R [auth D]
(5S)-2,5-dihydroxy-3-methylcyclohex-2-ene-1,4-dione
C7 H8 O4
CWBLUSPNRBEFNW-BYPYZUCNSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth B]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
H [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth C],
N [auth C],
P [auth D],
Q [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TR9 PDBBind:  3KQA IC50: 1.40e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.27α = 90
b = 115.27β = 90
c = 277.4γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
CNSrefinement
XDSdata reduction
XDSdata scaling
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: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-07-27
    Changes: Database references, Derived calculations, Non-polymer description
  • Version 1.3: 2023-09-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary