3ITA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-alanyl-D-alanine carboxypeptidase dacCA, B, C, D352Escherichia coliMutation(s): 0 
Gene Names: b0839dacCJW0823
EC: 3.4.16.4
UniProt
Find proteins for P08506 (Escherichia coli (strain K12))
Explore P08506 
Go to UniProtKB:  P08506
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AIX (Subject of Investigation/LOI)
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
WHAIWIUXAXKSOT-NRWUCQMLSA-N
 Ligand Interaction
AIC (Subject of Investigation/LOI)
Query on AIC

Download Ideal Coordinates CCD File 
L [auth D](2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID
C16 H19 N3 O4 S
AVKUERGKIZMTKX-NJBDSQKTSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

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