Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Tetrahedral - T  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.94 kDa 
• Atom Count: 3936 
• Residue Count: 442 
• Unique protein chains: 1

4AZS

High resolution (2.2 A) crystal structure of WbdD.

• DOI: 10.2210/pdb4AZS/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-06-26 Released: 2012-09-26 
• Deposition Author(s): Hagelueken, G., Huang, H., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.222 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Literature

Structure of Wbdd; a Bifunctional Kinase and Methyltransferase that Regulates the Chain Length of the O Antigen in Escherichia Coli O9A.

Hagelueken, G., Huang, H., Clarke, B.R., Lebl, T., Whitfield, C., Naismith, J.H.

(2012) Mol Microbiol 86: 730

• PubMed: 22970759 
• DOI: 10.1111/mmi.12014
• Primary Citation of Related Structures:  
  4AZV, 4AZW, 4AZS, 4AZT


• PubMed Abstract: 
  

The Escherichia coli serotype O9a O-antigen polysaccharide (O-PS) is a model for glycan biosynthesis and export by the ATP-binding cassette transporter-dependent pathway. The polymannose O9a O-PS is synthesized as a polyprenol-linked glycan by mannosyltransferase enzymes located at the cytoplasmic membrane. The chain length of the O9a O-PS is tightly regulated by the WbdD enzyme. WbdD first phosphorylates the terminal non-reducing mannose of the O-PS and then methylates the phosphate, stopping polymerization. The 2.2 Å resolution structure of WbdD reveals a bacterial methyltransferase domain joined to a eukaryotic kinase domain. The kinase domain is again fused to an extended C-terminal coiled-coil domain reminiscent of eukaryotic DMPK (Myotonic Dystrophy Protein Kinase) family kinases such as Rho-associated protein kinase (ROCK). WbdD phosphorylates 2-α-d-mannosyl-d-mannose (2α-MB), a short mimic of the O9a polymer. Mutagenesis identifies those residues important in catalysis and substrate recognition and the in vivo phenotypes of these mutants are used to dissect the termination reaction. We have determined the structures of co-complexes of WbdD with two known eukaryotic protein kinase inhibitors. Although these are potent inhibitors in vitro, they do not show any in vivo activity. The structures reveal new insight into O-PS chain-length regulation in this important model system.

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Organizational Affiliation: 

Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYLTRANSFERASE WBDD	A	569	Escherichia coli	Mutation(s): 0  Gene Names: wbdD, ORF708 EC: 2.1.1.294 (UniProt), 2.7.1.181 (UniProt)
Find proteins for Q47592 (Escherichia coli) Explore Q47592  Go to UniProtKB:  Q47592

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	A	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
AMP	A	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.222 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.22	α = 90
b = 159.22	β = 90
c = 159.22	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-26 
• Released Date: 2012-09-26 
Deposition Author(s): Hagelueken, G., Huang, H., Naismith, J.H.

Revision History 

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Database references