4OKP

Crystal structure of AmpC beta-lactamase in complex with the product form of 7-amino-desacetoxycephalosporanic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Substrate deconstruction and the nonadditivity of enzyme recognition.

Barelier, S., Cummings, J.A., Rauwerdink, A.M., Hitchcock, D.S., Farelli, J.D., Almo, S.C., Raushel, F.M., Allen, K.N., Shoichet, B.K.

(2014) J.Am.Chem.Soc. 136: 7374-7382

  • DOI: 10.1021/ja501354q
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Predicting substrates for enzymes of unknown function is a major postgenomic challenge. Substrate discovery, like inhibitor discovery, is constrained by our ability to explore chemotypes; it would be expanded by orders of magnitude if reactive sites ...

    Predicting substrates for enzymes of unknown function is a major postgenomic challenge. Substrate discovery, like inhibitor discovery, is constrained by our ability to explore chemotypes; it would be expanded by orders of magnitude if reactive sites could be probed with fragments rather than fully elaborated substrates, as is done for inhibitor discovery. To explore the feasibility of this approach, substrates of six enzymes from three different superfamilies were deconstructed into 41 overlapping fragments that were tested for activity or binding. Surprisingly, even those fragments containing the key reactive group had little activity, and most fragments did not bind measurably, until they captured most of the substrate features. Removing a single atom from a recognized substrate could often reduce catalytic recognition by 6 log-orders. To explore recognition at atomic resolution, the structures of three fragment complexes of the β-lactamase substrate cephalothin were determined by X-ray crystallography. Substrate discovery may be difficult to reduce to the fragment level, with implications for function discovery and for the tolerance of enzymes to metabolite promiscuity. Pragmatically, this study supports the development of libraries of fully elaborated metabolites as probes for enzyme function, which currently do not exist.

    Organizational Affiliation: 

    Department of Pharmaceutical Chemistry, University of California - San Francisco , 1700 Fourth Street, Byers Hall, San Francisco, California 94158, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B
358Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ampC (ampA)
EC: 3.5.2.6
Find proteins for P00811 (Escherichia coli (strain K12))
Go to UniProtKB:  P00811
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
2V0
Query on 2V0
Download SDF File 
Download CCD File 
B
(2R)-2-[(R)-amino(carboxy)methyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
7-aminodeacetoxycephalosporanic acid, hydrolyzed form
C8 H12 N2 O4 S
WFPVQOKEJDXMTD-UJURSFKZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.143 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 118.120α = 90.00
b = 76.490β = 115.85
c = 97.620γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
ADSCdata collection
XDSdata scaling
PHENIXrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-06-18
    Type: Database references