3FWL

Crystal Structure of the Full-Length Transglycosylase PBP1b from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli.

Sung, M.T.Lai, Y.T.Huang, C.Y.Chou, L.Y.Shih, H.W.Cheng, W.C.Wong, C.H.Ma, C.

(2009) Proc Natl Acad Sci U S A 106: 8824-8829

  • DOI: 10.1073/pnas.0904030106
  • Primary Citation of Related Structures:  
    3FWL, 3VMA

  • PubMed Abstract: 
  • Drug-resistant bacteria have caused serious medical problems in recent years, and the need for new antibacterial agents is undisputed. Transglycosylase, a multidomain membrane protein essential for cell wall synthesis, is an excellent target for the ...

    Drug-resistant bacteria have caused serious medical problems in recent years, and the need for new antibacterial agents is undisputed. Transglycosylase, a multidomain membrane protein essential for cell wall synthesis, is an excellent target for the development of new antibiotics. Here, we determined the X-ray crystal structure of the bifunctional transglycosylase penicillin-binding protein 1b (PBP1b) from Escherichia coli in complex with its inhibitor moenomycin to 2.16-A resolution. In addition to the transglycosylase and transpeptidase domains, our structure provides a complete visualization of this important antibacterial target, and reveals a domain for protein-protein interaction and a transmembrane helix domain essential for substrate binding, enzymatic activity, and membrane orientation.


    Organizational Affiliation

    Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Taipei 115, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Penicillin-binding protein 1BA751Escherichia coliMutation(s): 0 
Gene Names: b0149JW0145mrcBpbpFponB
EC: 2.4.1.129 (PDB Primary Data), 3.4 (PDB Primary Data), 3.4.16.4 (UniProt)
Membrane protein
Mpstruc
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Glycosyltransferases
Protein: 
Peptidoglycan Glycosyltransferase penicillin-binding protein 1b (PBP1b)
Find proteins for P02919 (Escherichia coli (strain K12))
Explore P02919 
Go to UniProtKB:  P02919
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M0E
Query on M0E

Download CCD File 
A
MOENOMYCIN
C69 H106 N5 O34 P
NXPRJQIAIORCGO-ZLPAOQQDSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.245α = 90
b = 296.997β = 90
c = 62.824γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description