4UA6

CTX-M-14 Class A Beta-Lactamase Apo Crystal Structure at 0.79 Angstrom Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.79 Å
  • R-Value Free: 0.115 
  • R-Value Work: 0.110 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Ligand-Induced Proton Transfer and Low-Barrier Hydrogen Bond Revealed by X-ray Crystallography.

Nichols, D.A.Hargis, J.C.Sanishvili, R.Jaishankar, P.Defrees, K.Smith, E.W.Wang, K.K.Prati, F.Renslo, A.R.Woodcock, H.L.Chen, Y.

(2015) J.Am.Chem.Soc. 137: 8086-8095

  • DOI: 10.1021/jacs.5b00749
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ligand binding can change the pKa of protein residues and influence enzyme catalysis. Herein, we report three ultrahigh resolution X-ray crystal structures of CTX-M β-lactamase, directly visualizing protonation state changes along the enzymatic pathw ...

    Ligand binding can change the pKa of protein residues and influence enzyme catalysis. Herein, we report three ultrahigh resolution X-ray crystal structures of CTX-M β-lactamase, directly visualizing protonation state changes along the enzymatic pathway: apo protein at 0.79 Å, precovalent complex with nonelectrophilic ligand at 0.89 Å, and acylation transition state (TS) analogue at 0.84 Å. Binding of the noncovalent ligand induces a proton transfer from the catalytic Ser70 to the negatively charged Glu166, and the formation of a low-barrier hydrogen bond (LBHB) between Ser70 and Lys73, with a length of 2.53 Å and the shared hydrogen equidistant from the heteroatoms. QM/MM reaction path calculations determined the proton transfer barrier to be 1.53 kcal/mol. The LBHB is absent in the other two structures although Glu166 remains neutral in the covalent complex. Our data represents the first X-ray crystallographic example of a hydrogen engaged in an enzymatic LBHB, and demonstrates that desolvation of the active site by ligand binding can provide a protein microenvironment conducive to LBHB formation. It also suggests that LBHBs may contribute to stabilization of the TS in general acid/base catalysis together with other preorganized features of enzyme active sites. These structures reconcile previous experimental results suggesting alternatively Glu166 or Lys73 as the general base for acylation, and underline the importance of considering residue protonation state change when modeling protein-ligand interactions. Additionally, the observation of another LBHB (2.47 Å) between two conserved residues, Asp233 and Asp246, suggests that LBHBs may potentially play a special structural role in proteins.


    Organizational Affiliation

    ‡Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States.,†Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States.,∥Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 1700 Fourth Street, Byers Hall S504, San Francisco, California 941584, United States.,§GMCA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States.,⊥Department of Life Sciences, University of Modena and Reggio Emilia, 41100 Modena, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase CTX-M-14
A, B
263Escherichia coliMutation(s): 0 
Gene Names: CTX-M-14
EC: 3.5.2.6
Find proteins for H6UQI0 (Escherichia coli)
Go to UniProtKB:  H6UQI0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.79 Å
  • R-Value Free: 0.115 
  • R-Value Work: 0.110 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.106α = 90.00
b = 106.581β = 102.23
c = 47.716γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SHELXLrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI103158

Revision History 

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-07-15
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Advisory, Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy
  • Version 2.0: 2019-12-11
    Type: Author supporting evidence, Polymer sequence