2G2U: Crystal Structure Of The Shv-1 Beta-lactamase/beta-lactamase Inhibitor Protein (blip) Complex

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.
PDB ID: 2G2UDownload
MMDB ID: 39935
PDB Deposition Date: 2006/2/16
Updated in MMDB: 2017/10
Experimental Method:
x-ray diffraction
Resolution: 1.6  Å
Source Organism:
Streptomyces clavuligerus
Similar Structures:
Biological Unit for 2G2U: dimeric; determined by author and by software (PISA)
Molecular Components in 2G2U
Label Count Molecule
Proteins (2 molecules)
Beta-lactamase Shv-1
Molecule annotation
Beta-lactamase Inhibitory Protein
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB