PDBsum entry 3c7v

Hydrolase/hydrolase inhibitor

PDB id: 3c7v

Contents

Protein chains

263 a.a. *

165 a.a. *

Waters ×173

* Residue conservation analysis

PDB id:

3c7v

Name:

Hydrolase/hydrolase inhibitor

Title:

Structural insight into the kinetics and delta-cp of interactions between tem-1 beta-lactamase and blip

Structure:

Beta-lactamase. Chain: a, c. Synonym: extended spectrum beta-lactamase, tem extended spectrum beta-lactamase, betalactamase tem-116, mutant extended- spectrum beta-lactamase, beta lactamase. Engineered: yes. Mutation: yes. Beta-lactamase inhibitory protein. Chain: b, d.

Source:

Escherichia coli. Organism_taxid: 562. Gene: bla, blatem-116. Expressed in: escherichia coli. Expression_system_taxid: 562. Streptomyces clavuligerus. Organism_taxid: 1901. Expression_system_taxid: 562

Resolution:

2.07Å R-factor: 0.216 R-free: 0.238

Authors:

J.Wang,D.-C.Chow

Key ref:

J.Wang et al. (2009). Structural Insight into the Kinetics and {Delta}Cp of Interactions between TEM-1 {beta}-Lactamase and {beta}-Lactamase Inhibitory Protein (BLIP). J Biol Chem, 284, 595-609. PubMed id: 18840610 DOI: 10.1074/jbc.M804089200

Date:

08-Feb-08 Release date: 07-Oct-08

Protein chains

P62593  (BLAT_ECOLX) -  Beta-lactamase TEM from Escherichia coli

Seq: 286 a.a.

Struc: 263 a.a.*

Protein chains

P35804  (BLIP_STRCL) -  Beta-lactamase inhibitory protein from Streptomyces clavuligerus

Seq: 201 a.a.

Struc: 165 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, C: E.C.3.5.2.6 - beta-lactamase.
• Pathway: Penicillin Biosynthesis and Metabolism
• Reaction: a beta-lactam + H2O = a substituted beta-amino acid
• Cofactor: Zn(2+)

DOI no: 10.1074/jbc.M804089200

J Biol Chem 284:595-609 (2009)

PubMed id: 18840610

Structural Insight into the Kinetics and {Delta}Cp of Interactions between TEM-1 {beta}-Lactamase and {beta}-Lactamase Inhibitory Protein (BLIP).

J.Wang, T.Palzkill, D.C.Chow.

ABSTRACT

In a previous study, we examined thermodynamic parameters for 20 alanine mutants inbeta-lactamase inhibitory protein (BLIP) for binding to TEM-1 beta-lactamase. Here we have determined the structures of two thermodynamically distinctive complexes of BLIP mutants with TEM-1 beta-lactamase. The complex BLIP Y51A-TEM-1 is a tight binding complex with the most negative binding heat capacity change (DeltaG = approximately -13 kcal mol(-1) and DeltaCp = approximately -0.8 kcal mol(-1) K(-1)) among all of the mutants, whereas BLIP W150A-TEM-1 is a weak complex with one of the least negative binding heat capacity changes (DeltaG = approximately -8.5 kcal mol(-1) and DeltaCp = approximately -0.27 kcal mol(-1) K(-1)). We previously determined that BLIP Tyr(51) is a canonical and Trp(150) an anti-canonical TEM-1-contact residue, where canonical refers to the alanine substitution resulting in a matched change in the hydrophobicity of binding free energy. Structure determination indicates a rearrangement of the interactions between Asp(49) of the W150A BLIP mutant and the catalytic pocket of TEM-1. The Asp(49) of W150A moves more than 4 A to form two new hydrogen bonds while losing four original hydrogen bonds. This explains the anti-canonical nature of the Trp(150) to alanine substitution, and also reveals a strong long distance coupling between Trp(150) and Asp(49) of BLIP, because these two residues are more than 25 A apart. Kinetic measurements indicate that the mutations influence the dissociation rate but not the association rate. Further analysis of the structures indicates that an increased number of interface-trapped water molecules correlate with poor interface packing in a mutant. It appears that the increase of interface-trapped water molecules is inversely correlated with negative binding heat capacity changes.

Selected figure(s)

Figure 3.
Analysis of interface-trapped water molecules. A, locations of all the identified water molecules in the crystal structures of Y51A-TEM-1 and of W150A-TEM-1 complexes. The complexes were superposed using SUPERPOSE in the CCP4 package. TEM-1 is represented as orange tubes, and the BLIP mutant is in green schematic representation. Green CPK balls are the identified water molecules from the AB complex of W150A-TEM-1 crystal structure, and green dotted circles represent water molecules from the CD complex. Red CPK balls are the identified water molecules from the AB complex of Y51A-TEM-1 crystal structure, and red dotted circles are the water molecules from the CD complex of Y51A-TEM-1 crystal. B, locations of the identified interfacial water molecules on the surface of the BLIP mutants. The BLIP mutants are represented as molecular surfaces. The interfacial water molecules are represented as red balls (for the AB complex in the asymmetric unit) or as dotted spheres (for the CD complex in the asymmetric unit). The W150A-TEM-1 complex is at left, the wild type complex is at center, and to the right is the Y51A-TEM-1 complex. C, histogram of the identified electron density peaks within the BLIP mutant-TEM-1 interfaces. The electron density peaks with B values less than 50 Å^2 are assigned as water.

Figure 4.
Plot of the number of the selected intermolecular atom pairs located within various distance ranges from the TEM-1 surface versus the distance. Selection criterion is the shortest intermolecular atom pairs for each BLIP atom. The solid thick line with the square symbols indicates the intermolecular atom pair distribution of the Y51A-TEM-1 complex that is 20% denser than W150A-TEM-1 complex (thin line with circle symbols) at ∼3.6 Å.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2009, 284, 595-609) copyright 2009.

Figures were selected by an automated process.