3N4I

Crystal structure of the SHV-1 D104E beta-lactamase/beta-lactamase inhibitor protein (BLIP) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Specificity and Cooperativity at beta-lactamase Position 104 in TEM-1/BLIP and SHV-1/BLIP interactions

Hanes, M.S.Reynolds, K.A.McNamara, C.Ghosh, P.Bonomo, R.A.Kirsch, J.F.Handel, T.M.

(2011) Proteins 79: 1267-1276

  • DOI: 10.1002/prot.22961
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Establishing a quantitative understanding of the determinants of affinity in protein-protein interactions remains challenging. For example, TEM-1/β-lactamase inhibitor protein (BLIP) and SHV-1/BLIP are homologous β-lactamase/β-lactamase inhibitor pro ...

    Establishing a quantitative understanding of the determinants of affinity in protein-protein interactions remains challenging. For example, TEM-1/β-lactamase inhibitor protein (BLIP) and SHV-1/BLIP are homologous β-lactamase/β-lactamase inhibitor protein complexes with disparate K(d) values (3 nM and 2 μM, respectively), and a single substitution, D104E in SHV-1, results in a 1000-fold enhancement in binding affinity. In TEM-1, E104 participates in a salt bridge with BLIP K74, whereas the corresponding SHV-1 D104 does not in the wild type SHV-1/BLIP co-structure. Here, we present a 1.6 Å crystal structure of the SHV-1 D104E/BLIP complex that demonstrates that this point mutation restores this salt bridge. Additionally, mutation of a neighboring residue, BLIP E73M, results in salt bridge formation between SHV-1 D104 and BLIP K74 and a 400-fold increase in binding affinity. To understand how this salt bridge contributes to complex affinity, the cooperativity between the E/K or D/K salt bridge pair and a neighboring hot spot residue (BLIP F142) was investigated using double mutant cycle analyses in the background of the E73M mutation. We find that BLIP F142 cooperatively stabilizes both interactions, illustrating how a single mutation at a hot spot position can drive large perturbations in interface stability and specificity through a cooperative interaction network.


    Organizational Affiliation

    Biophysics Graduate Group, University of California, Berkeley, Berkeley, California 94729, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase SHV-1A265Klebsiella pneumoniaeMutation(s): 1 
Gene Names: blabla SHV1RSMK03643RSMK03800shv1
EC: 3.5.2.6
Find proteins for P0AD64 (Klebsiella pneumoniae)
Explore P0AD64 
Go to UniProtKB:  P0AD64
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase inhibitory proteinB165Streptomyces clavuligerusMutation(s): 0 
Gene Names: bli
Find proteins for P35804 (Streptomyces clavuligerus)
Explore P35804 
Go to UniProtKB:  P35804
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.85α = 90
b = 127.85β = 90
c = 73.183γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
JBluIce-EPICSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-06-19
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description