3A3E

Crystal structure of penicillin binding protein 4 (dacB) from Haemophilus influenzae, complexed with novel beta-lactam (CMV)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

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This is version 1.3 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: https://doi.org/10.1016/j.jmb.2009.11.055
  • Primary Citation of Related Structures:  
    3A3D, 3A3E, 3A3F, 3A3I, 3A3J

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein 4
A, B
453Haemophilus influenzaeMutation(s): 0 
Gene Names: dacB
EC: 3.4.16.4
UniProt
Find proteins for A8E0K8 (Haemophilus influenzae)
Explore A8E0K8 
Go to UniProtKB:  A8E0K8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8E0K8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CMV
Query on CMV

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2R,4S)-2-[(1R)-1-({(2R)-2-[(4-ethyl-2,3-dioxopiperazin-1-yl)amino]-2-phenylacetyl}amino)-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
C22 H29 N5 O6 S
FLMJTSOTBGMFLJ-XLMAVXFVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.898α = 90
b = 92.823β = 107.79
c = 104.173γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-11-20
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Structure summary