3VMA

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

• PDB DOI: https://doi.org/10.2210/pdb3VMA/pdb
• Entry: 3VMA supersedes: 3FWM

• Classification: TRANSFERASE, HYDROLASE/ANTIBIOTIC
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2011-12-09 Released: 2012-03-14 
• Deposition Author(s): Huang, C.Y., Sung, M.T., Lai, Y.T., Chou, L.Y., Shih, H.W., Cheng, W.C., Wong, C.H., Ma, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.250 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Starting Model: experimental

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

• PubMed: 19458048 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 87.16 kDa 
• Atom Count: 5,855 
• Modelled Residue Count: 708 
• Deposited Residue Count: 768 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 1B	A	768	Escherichia coli K-12	Mutation(s): 0  Gene Names: b0149, JW0145, mrcB, pbpF, ponB EC: 2.4.1.129 (PDB Primary Data), 3.4 (PDB Primary Data), 2.4.99.28 (UniProt), 3.4.16.4 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P02919 (Escherichia coli (strain K12)) Explore P02919  Go to UniProtKB:  P02919

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M0E	B [auth A]	MOENOMYCIN C69 H106 N5 O34 P NXPRJQIAIORCGO-ZLPAOQQDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.250 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.9	α = 90
b = 289.53	β = 90
c = 62.78	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-14 
Deposition Author(s): Huang, C.Y., Sung, M.T., Lai, Y.T., Chou, L.Y., Shih, H.W., Cheng, W.C., Wong, C.H., Ma, C.
• This entry supersedes: 3FWM

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description