2G2W

Crystal Structure of the SHV D104K Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) complex

Summary for 2G2W

• Entry DOI: 10.2210/pdb2g2w/pdb
• Related: 2G2U
• Descriptor: Beta-lactamase SHV-1, Beta-lactamase inhibitory protein (3 entities in total)
• Functional Keywords: beta-lactamase, beta-lactamase inhibitor, protein-protein complex, blip, shv, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Klebsiella pneumoniae; More
• Cellular location: Secreted: P35804
• Total number of polymer chains: 2
• Total formula weight: 46477.60

Authors

Reynolds, K.A.,Thomson, J.M.,Corbett, K.D.,Bethel, C.R.,Berger, J.M.,Kirsch, J.F.,Bonomo, R.A.,Handel, T.M. (deposition date: 2006-02-16, release date: 2006-07-04, Last modification date: 2023-08-30)

Primary citation

Reynolds, K.A.,Thomson, J.M.,Corbett, K.D.,Bethel, C.R.,Berger, J.M.,Kirsch, J.F.,Bonomo, R.A.,Handel, T.M.
Structural and Computational Characterization of the SHV-1 beta-Lactamase-beta-Lactamase Inhibitor Protein Interface.
J.Biol.Chem., 281:26745-26753, 2006

PubMed Abstract: Beta-lactamase inhibitor protein (BLIP) binds a variety of class A beta-lactamases with affinities ranging from micromolar to picomolar. Whereas the TEM-1 and SHV-1 beta-lactamases are almost structurally identical, BLIP binds TEM-1 approximately 1000-fold tighter than SHV-1. Determining the underlying source of this affinity difference is important for understanding the molecular basis of beta-lactamase inhibition and mechanisms of protein-protein interface specificity and affinity. Here we present the 1.6A resolution crystal structure of SHV-1.BLIP. In addition, a point mutation was identified, SHV D104E, that increases SHV.BLIP binding affinity from micromolar to nanomolar. Comparison of the SHV-1.BLIP structure with the published TEM-1.BLIP structure suggests that the increased volume of Glu-104 stabilizes a key binding loop in the interface. Solution of the 1.8A SHV D104K.BLIP crystal structure identifies a novel conformation in which this binding loop is removed from the interface. Using these structural data, we evaluated the ability of EGAD, a program developed for computational protein design, to calculate changes in the stability of mutant beta-lactamase.BLIP complexes. Changes in binding affinity were calculated within an error of 1.6 kcal/mol of the experimental values for 112 mutations at the TEM-1.BLIP interface and within an error of 2.2 kcal/mol for 24 mutations at the SHV-1.BLIP interface. The reasonable success of EGAD in predicting changes in interface stability is a promising step toward understanding the stability of the beta-lactamase.BLIP complexes and computationally assisted design of tight binding BLIP variants.

PubMed: 16809340
DOI: 10.1074/jbc.M603878200

Experimental method

X-RAY DIFFRACTION (1.8 Å)