3P98 | pdb_00003p98

The crystal structure of the extended spectrum beta-lactamase TEM-72 reveals inhibition by citrate

• PDB DOI: https://doi.org/10.2210/pdb3P98/pdb

• Classification: HYDROLASE
• Organism(s): Morganella morganii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-16 Released: 2011-03-09 
• Deposition Author(s): Docquier, J.D., Benvenuti, M., Calderone, V., Rossolini, G.M., Mangani, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.283 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.201 (Depositor) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Structure of the extended-spectrum [beta]-lactamase TEM-72 inhibited by citrate

Docquier, J.D., Benvenuti, M., Calderone, V., Rossolini, G.M., Mangani, S.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 303-306

• PubMed: 21393831 
• DOI: https://doi.org/10.1107/S1744309110054680
• Primary Citation Related Structures: 
  3P98


• PubMed Abstract: 
  

  TEM-72, a class A β-lactamase identified in isolates of Enterobacteriaceae, is a quadruple mutant of TEM-1 (Q39K, M182T, G238S and E240K) and shows extended-spectrum β-lactamase (ESBL) properties arising from the G238S and E240K substitutions. Although many structures of TEM variants have been published, they do not include an enzyme with the simultaneous presence of both of the ESBL-conferring G238S and E240K substitutions. Furthermore, the structure shows the presence of a citrate anion bound to the TEM-72 active site, where it interacts with all of the conserved residues of class A β-lactamases. The present structure supports the use of polycarboxylates as a scaffold for the design of broad-spectrum inhibitors of serine β-lactamases.

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Organizational Affiliation: 
• Dipartimento di Biologia Molecolare, Laboratorio di Fisiologia e Biotecnologia dei Microrganismi, Università di Siena, I-53100 Siena, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.7 kDa 
• Atom Count: 4,341 
• Modeled Residue Count: 526 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase TEM-72	A, B	286	Morganella morganii	Mutation(s): 0  EC: 3.5.2.6
UniProt
Find proteins for Q9R429 (Morganella morganii) Explore Q9R429  Go to UniProtKB:  Q9R429

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], E [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
PEG	D [auth A], F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.283 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.201 (Depositor) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.63	α = 90
b = 90.212	β = 90
c = 96.047	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-09 
Deposition Author(s): Docquier, J.D., Benvenuti, M., Calderone, V., Rossolini, G.M., Mangani, S.

Revision History  

• Version 1.0: 2011-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-21
  Changes: Database references
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-27
  Changes: Structure summary