Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in acyl-enzyme complex with ampicillin

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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Crystal structures of penicillin-binding protein 6 from Escherichia coli.

Chen, Y.Zhang, W.Shi, Q.Hesek, D.Lee, M.Mobashery, S.Shoichet, B.K.

(2009) J Am Chem Soc 131: 14345-14354

  • DOI: https://doi.org/10.1021/ja903773f
  • Primary Citation of Related Structures:  
    3IT9, 3ITA, 3ITB

  • PubMed Abstract: 

    Penicillin-binding protein 6 (PBP6) is one of the two main DD-carboxypeptidases in Escherichia coli, which are implicated in maturation of bacterial cell wall and formation of cell shape. Here, we report the first X-ray crystal structures of PBP6, capturing its apo state (2.1 A), an acyl-enzyme intermediate with the antibiotic ampicillin (1.8 A), and for the first time for a PBP, a preacylation complex (a "Michaelis complex", determined at 1.8 A) with a peptidoglycan substrate fragment containing the full pentapeptide, NAM-(L-Ala-D-isoGlu-L-Lys-D-Ala-D-Ala). These structures illuminate the molecular interactions essential for ligand recognition and catalysis by DD-carboxypeptidases, and suggest a coupling of conformational flexibility of active site loops to the reaction coordinate. The substrate fragment complex structure, in particular, provides templates for models of cell wall recognition by PBPs, as well as substantiating evidence for the molecular mimicry by beta-lactam antibiotics of the peptidoglycan acyl-D-Ala-D-Ala moiety.

  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California San Francisco, Byers Hall, Room 508D, 1700 Fourth Street, San Francisco, California 94158-2550, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-alanyl-D-alanine carboxypeptidase dacC
A, B, C, D
352Escherichia coliMutation(s): 0 
Gene Names: b0839dacCJW0823
Find proteins for P08506 (Escherichia coli (strain K12))
Explore P08506 
Go to UniProtKB:  P08506
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08506
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AIX

Download Ideal Coordinates CCD File 
E [auth A](2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
C16 H21 N3 O4 S
Query on AIC

Download Ideal Coordinates CCD File 
C16 H19 N3 O4 S
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth B]
H [auth B]
I [auth C]
J [auth C]
F [auth A],
G [auth B],
H [auth B],
I [auth C],
J [auth C],
K [auth C]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.938α = 90
b = 185.98β = 101.37
c = 83.036γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description