3CMZ | pdb_00003cmz

TEM-1 Class-A beta-lactamase L201P mutant apo structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 
    0.242 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

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

Literature

Genetic and structural characterization of an L201P global suppressor substitution in TEM-1 beta-lactamase

Marciano, D.C.Pennington, J.M.Wang, X.Wang, J.Chen, Y.Thomas, V.L.Shoichet, B.K.Palzkill, T.

(2008) J Mol Biology 384: 151-164

  • DOI: https://doi.org/10.1016/j.jmb.2008.09.009
  • Primary Citation Related Structures: 
    3CMZ

  • PubMed Abstract: 

    TEM-1 beta-lactamase confers bacterial resistance to penicillin antibiotics and has acquired mutations that permit the enzyme to hydrolyze extended-spectrum cephalosporins or to avoid inactivation by beta-lactamase inhibitors. However, many of these substitutions have been shown to reduce activity against penicillin antibiotics and/or result in loss of stability for the enzyme. In order to gain more information concerning the tradeoffs associated with active site substitutions, a genetic selection was used to find second site mutations that partially restore ampicillin resistance levels conferred by an R244A active site TEM-1 beta-lactamase mutant. An L201P substitution distant from the active site that enhanced ampicillin resistance levels and increased protein expression levels of the R244A TEM-1 mutant was identified. The L201P substitution also increases the ampicillin resistance levels and restores expression levels of a poorly expressed TEM-1 mutant with a core-disrupting substitution. In vitro thermal denaturation of purified protein indicated that the L201P mutation increases the T(m) value of the TEM-1 enzyme. The X-ray structure of the L201P TEM-1 mutant was determined to gain insight into the increase in enzyme stability. The proline substitution occurs at the N-terminus of an alpha-helix and may stabilize the enzyme by reducing the helix dipole, as well as by lowering the conformational entropy cost of folding due to the reduced number of conformations available in the unfolded state. Collectively, the data suggest that L201P promotes tolerance of some deleterious TEM-1 mutations by enhancing the protein stability of these mutants.


  • Organizational Affiliation
    • Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.

Macromolecule Content 

  • Total Structure Weight: 29.02 kDa 
  • Atom Count: 2,154 
  • Modeled Residue Count: 263 
  • Deposited Residue Count: 263 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase TEM263Escherichia coliMutation(s): 1 
Gene Names: bla
EC: 3.5.2.6
UniProt
Find proteins for P62593 (Escherichia coli)
Explore P62593 
Go to UniProtKB:  P62593
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62593
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.242 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.218α = 90
b = 59.14β = 90
c = 87.802γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary