Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.77 kDa 
• Atom Count: 1622 
• Residue Count: 181 
• Unique protein chains: 1

2OQO

Crystal structure of a peptidoglycan glycosyltransferase from a class A PBP: insight into bacterial cell wall synthesis

• DOI: 10.2210/pdb2OQO/pdb

• Classification: TRANSFERASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-01-31 Released: 2007-03-13 
• Deposition Author(s): Yuan, Y., Sliz, P., Walker, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.244 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

Crystal structure of a peptidoglycan glycosyltransferase suggests a model for processive glycan chain synthesis.

Yuan, Y., Barrett, D., Zhang, Y., Kahne, D., Sliz, P., Walker, S.

(2007) Proc Natl Acad Sci U S A 104: 5348-5353

• PubMed: 17360321 
• DOI: 10.1073/pnas.0701160104
• Primary Citation of Related Structures:  
  2OQO


• PubMed Abstract: 
  

Peptidoglycan is an essential polymer that forms a protective shell around bacterial cell membranes. Peptidoglycan biosynthesis is the target of many clinically used antibiotics, including the beta-lactams, imipenems, cephalosporins, and glycopeptides. Resistance to these and other antibiotics has prompted interest in an atomic-level understanding of the enzymes that make peptidoglycan. Representative structures have been reported for most of the enzymes in the pathway. Until now, however, there have been no structures of any peptidoglycan glycosyltransferases (also known as transglycosylases), which catalyze formation of the carbohydrate chains of peptidoglycan from disaccharide subunits on the bacterial cell surface. We report here the 2.1-A crystal structure of the peptidoglycan glycosyltransferase (PGT) domain of Aquifex aeolicus PBP1A. The structure has a different fold from all other glycosyltransferase structures reported to date, but it bears some resemblance to lambda-lysozyme, an enzyme that degrades the carbohydrate chains of peptidoglycan. An analysis of the structure, combined with biochemical information showing that these enzymes are processive, suggests a model for glycan chain polymerization.

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Organizational Affiliation: 

Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 1A (PBP-1a) (PBP1a)	A	200	Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: mrcA, ponA, aq_624 EC: 2.4.2 (PDB Primary Data), 2.4.1.129 (UniProt), 3.4.16.4 (UniProt)
Membrane protein Mpstruc	Group:  MONOTOPIC MEMBRANE PROTEINS		Sub Group:  Glycosyltransferases	Protein:  Peptidoglycan Glycosyltransferase penicillin-binding protein 1a (PBP1a)
Find proteins for O66874 (Aquifex aeolicus (strain VF5)) Explore O66874  Go to UniProtKB:  O66874

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPS	A	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE C32 H58 N2 O7 S UMCMPZBLKLEWAF-BCTGSCMUSA-N
EPE	A	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.244 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.817	α = 90
b = 100.305	β = 90
c = 104.012	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-31 
• Released Date: 2007-03-13 
Deposition Author(s): Yuan, Y., Sliz, P., Walker, S.

Revision History 

• Version 1.0: 2007-03-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description