Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 46.46 kDa 
• Atom Count: 3590 
• Residue Count: 430 
• Unique protein chains: 2

2G2U

Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) complex

• DOI: 10.2210/pdb2G2U/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Klebsiella pneumoniae, Streptomyces clavuligerus
• Expression System: Escherichia coli str. K-12 substr. DH10B, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-02-16 Released: 2006-07-04 
• Deposition Author(s): Reynolds, K.A., Thomson, J.M., Corbett, K.D., Bethel, C.R., Berger, J.M., Kirsch, J.F., Bonomo, R.A., Handel, T.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.186 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Literature

Structural and Computational Characterization of the SHV-1 beta-Lactamase-beta-Lactamase Inhibitor Protein Interface.

Reynolds, K.A., Thomson, J.M., Corbett, K.D., Bethel, C.R., Berger, J.M., Kirsch, J.F., Bonomo, R.A., Handel, T.M.

(2006) J Biol Chem 281: 26745-26753

• PubMed: 16809340 
• DOI: 10.1074/jbc.M603878200
• Primary Citation of Related Structures:  
  2G2W, 2G2U


• 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.

---

Organizational Affiliation: 

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0684, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase SHV-1	A	265	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: bla, shv1 EC: 3.5.2.6
Find proteins for P0AD64 (Klebsiella pneumoniae) Explore P0AD64  Go to UniProtKB:  P0AD64

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase inhibitory protein	B	165	Streptomyces clavuligerus	Mutation(s): 0
Find proteins for P35804 (Streptomyces clavuligerus) Explore P35804  Go to UniProtKB:  P35804

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.186 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.871	α = 90
b = 127.871	β = 90
c = 73.4	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-16 
• Released Date: 2006-07-04 
Deposition Author(s): Reynolds, K.A., Thomson, J.M., Corbett, K.D., Bethel, C.R., Berger, J.M., Kirsch, J.F., Bonomo, R.A., Handel, T.M.

Revision History 

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description