3A3I

Crystal structure of penicillin binding protein 4 (dacB) from Haemophilus influenzae, complexed with ampicillin (AIX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of penicillin-binding proteins 4 and 5 from Haemophilus influenzae

Kawai, F.Clarke, T.B.Roper, D.I.Han, G.-J.Hwang, K.Y.Unzai, S.Obayashi, E.Park, S.-Y.Tame, J.R.H.

(2010) J.Mol.Biol. 396: 634-645

  • DOI: 10.1016/j.jmb.2009.11.055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have determined high-resolution apo crystal structures of two low molecular weight penicillin-binding proteins (PBPs), PBP4 and PBP5, from Haemophilus influenzae, one of the most frequently found pathogens in the upper respiratory tract of childre ...

    We have determined high-resolution apo crystal structures of two low molecular weight penicillin-binding proteins (PBPs), PBP4 and PBP5, from Haemophilus influenzae, one of the most frequently found pathogens in the upper respiratory tract of children. Novel beta-lactams with notable antimicrobial activity have been designed, and crystal structures of PBP4 complexed with ampicillin and two of the novel molecules have also been determined. Comparing the apo form with those of the complexes, we find that the drugs disturb the PBP4 structure and weaken X-ray diffraction, to very different extents. PBP4 has recently been shown to act as a sensor of the presence of penicillins in Pseudomonas aeruginosa, and our models offer a clue to the structural basis for this effect. Covalently attached penicillins press against a phenylalanine residue near the active site and disturb the deacylation step. The ready inhibition of PBP4 by beta-lactams compared to PBP5 also appears to be related to the weaker interactions holding key residues in a catalytically competent position.


    Organizational Affiliation

    Yokohama City University, Suehiro 1-7-29, Tsurumi, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Penicillin-binding protein 4
A, B
453Haemophilus influenzaeMutation(s): 0 
Gene Names: dacB
Find proteins for A8E0K8 (Haemophilus influenzae)
Go to UniProtKB:  A8E0K8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AIX
Query on AIX

Download SDF File 
Download CCD File 
A, B
(2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
AMPICILLIN (open form)
C16 H21 N3 O4 S
WHAIWIUXAXKSOT-NRWUCQMLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.449α = 90.00
b = 92.343β = 107.66
c = 104.409γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-11-20
    Type: Database references