3BEC

Crystal structure of E. coli penicillin-binding protein 5 in complex with a peptide-mimetic cephalosporin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Literature

Crystal structures of complexes of bacterial DD-peptidases with peptidoglycan-mimetic ligands: the substrate specificity puzzle

Sauvage, E., Powell, A.J., Heilemann, J., Josephine, H.R., Charlier, P., Davies, C., Pratt, R.F.

(2008) J Mol Biol 381: 383-393

  • DOI: 10.1016/j.jmb.2008.06.012
  • Primary Citation of Related Structures:  
    2VGJ, 2VGK, 3BEB, 3BEC

  • PubMed Abstract: 

    • The X-ray crystal structures of covalent complexes of the Actinomadura R39 dd-peptidase and Escherichia coli penicillin-binding protein (PBP) 5 with beta-lactams bearing peptidoglycan-mimetic side chains have been determined. The structure of the hydrolysis product of an analogous peptide bound noncovalently to the former enzyme has also been obtained ...

    The X-ray crystal structures of covalent complexes of the Actinomadura R39 dd-peptidase and Escherichia coli penicillin-binding protein (PBP) 5 with beta-lactams bearing peptidoglycan-mimetic side chains have been determined. The structure of the hydrolysis product of an analogous peptide bound noncovalently to the former enzyme has also been obtained. The R39 DD-peptidase structures reveal the presence of a specific binding site for the D-alpha-aminopimelyl side chain, characteristic of the stem peptide of Actinomadura R39. This binding site features a hydrophobic cleft for the pimelyl methylene groups and strong hydrogen bonding to the polar terminus. Both of these active site elements are provided by amino acid side chains from two separate domains of the protein. In contrast, no clear electron density corresponding to the terminus of the peptidoglycan-mimetic side chains is present when these beta-lactams are covalently bound to PBP5. There is, therefore, no indication of a specific side-chain binding site in this enzyme. These results are in agreement with those from kinetics studies published earlier and support the general prediction made at the time of a direct correlation between kinetics and structural evidence. The essential high-molecular-mass PBPs have demonstrated, to date, no specific reactivity with peptidoglycan-mimetic peptide substrates and beta-lactam inhibitors and, thus, probably do not possess a specific substrate-binding site of the type demonstrated here with the R39 DD-peptidase. This striking deficiency may represent a sophisticated defense mechanism against low-molecular-mass substrate-analogue inhibitors/antibiotics; its discovery should focus new inhibitor design.

    Organizational Affiliation: 

    Centre d'Ingéniere des Proteines, Université de Liège, B-4000 Sart Tilman, Liège, Belgium.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Penicillin-binding protein 5A363Escherichia coliMutation(s): 0 
Gene Names: dacA, pfv
EC: 3.4.16.4 (PDB Primary Data), 3.5.2.6 (PDB Primary Data)
UniProt
Find proteins for P0AEB2 (Escherichia coli (strain K12))
Explore P0AEB2 
Go to UniProtKB:  P0AEB2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEB2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HJ2
Query on HJ2
Download Ideal Coordinates CCD File 
C [auth A](2R)-2-[(R)-{[(6S)-6-amino-6-carboxyhexanoyl]amino}(carboxy)methyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
C15 H23 N3 O7 S
HJUSKFHSSKMVMT-KPXOXKRLSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
B [auth A],
D [auth A],
E [auth A],
F [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.5α = 90
b = 50.5β = 121.1
c = 85.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SERGUIdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance