Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51510.08 
• Atom Count: 3464 
• Residue Count: 456 
• Unique protein chains: 1

1DD6

IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH A MERCAPTOCARBOXYLATE INHIBITOR

• DOI: 10.2210/pdb1DD6/pdb

• Classification: HYDROLASE
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli BL21


• Deposited: 1999-11-08 Released: 2000-11-08 
• Deposition Author(s): Concha, N.O., Janson, C.A., Rowling, P., Pearson, S., Cheever, C.A., Clarke, B.P., Lewis, C., Galleni, M., Frere, J.M., Payne, D.J., Bateson, J.H., Abdel-Meguid, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.259 
• R-Value Work: 0.198 

Literature

Crystal structure of the IMP-1 metallo beta-lactamase from Pseudomonas aeruginosa and its complex with a mercaptocarboxylate inhibitor: binding determinants of a potent, broad-spectrum inhibitor.

Concha, N.O., Janson, C.A., Rowling, P., Pearson, S., Cheever, C.A., Clarke, B.P., Lewis, C., Galleni, M., Frere, J.M., Payne, D.J., Bateson, J.H., Abdel-Meguid, S.S.

(2000) Biochemistry 39: 4288-4298

• PubMed: 10757977 
• Primary Citation of Related Structures:  
  1DDK


• PubMed Abstract: 
  

Metallo beta-lactamase enzymes confer antibiotic resistance to bacteria by catalyzing the hydrolysis of beta-lactam antibiotics. This relatively new form of resistance is spreading unchallenged as there is a current lack of potent and selective inhibitors of metallo beta-lactamases. Reported here are the crystal structures of the native IMP-1 metallo beta-lactamase from Pseudomonas aeruginosa and its complex with a mercaptocarboxylate inhibitor, 2-[5-(1-tetrazolylmethyl)thien-3-yl]-N-[2-(mercaptomethyl)-4 -(phenylb utyrylglycine)]. The structures were determined by molecular replacement, and refined to 3.1 A (native) and 2.0 A (complex) resolution. Binding of the inhibitor in the active site induces a conformational change that results in closing of the flap and transforms the active site groove into a tunnel-shaped cavity enclosing 83% of the solvent accessible surface area of the inhibitor. The inhibitor binds in the active site through interactions with residues that are conserved among metallo beta-lactamases; the inhibitor's carboxylate group interacts with Lys161, and the main chain amide nitrogen of Asn167. In the "oxyanion hole", the amide carbonyl oxygen of the inhibitor interacts through a water molecule with the side chain of Asn167, the inhibitor's thiolate bridges the two Zn(II) ions in the active site displacing the bridging water, and the phenylbutyryl side chain binds in a hydrophobic pocket (S1) at the base of the flap. The flap is displaced 2.9 A compared to the unbound structure, allowing Trp28 to interact edge-to-face with the inhibitor's thiophene ring. The similarities between this inhibitor and the beta-lactam substrates suggest a mode of substrate binding and the role of the conserved residues in the active site. It appears that the metallo beta-lactamases bind their substrates by establishing a subset of binding interactions near the catalytic center with conserved characteristic chemical groups of the beta-lactam substrates. These interactions are complemented by additional nonspecific binding between the more variable groups in the substrates and the flexible flap. This unique mode of binding of the mercaptocarboxylate inhibitor in the enzyme active site provides a binding model for metallo beta-lactamase inhibition with utility for future drug design.

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Organizational Affiliation: 

Department of Structural Biology, SmithKline Beecham Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
IMP-1 METALLO BETA-LACTAMASE	A, B	228	Serratia marcescens	Mutation(s): 0  EC: 3.5.2.6
Find proteins for P52699 (Serratia marcescens) Go to UniProtKB:  P52699

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MCI	A, B	(2-MERCAPTOMETHYL-4-PHENYL-BUTYRYLIMINO)-(5-TETRAZOL-1-YLMETHYL-THIOPHEN-2-YL)-ACETIC ACID MERCAPTOCARBOXYLATE INHIBITOR C19 H19 N5 O3 S2 DUKDFMPUZRDWLT-CQSZACIVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.259 
• R-Value Work: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 49.300	α = 90.00
b = 51.200	β = 90.00
c = 203.300	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
AMoRE	phasing
SCALEPACK	data scaling
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-11-08 
• Released Date: 2000-11-08 
• Deposition Author(s): Concha, N.O., Janson, C.A., Rowling, P., Pearson, S., Cheever, C.A., Clarke, B.P., Lewis, C., Galleni, M., Frere, J.M., Payne, D.J., Bateson, J.H., Abdel-Meguid, S.S.

Revision History 

• Version 1.0: 2000-11-08
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-04
  Type: Refinement description
• Version 1.4: 2017-10-11
  Type: Data collection