Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 74.49 kDa 
• Atom Count: 5459 
• Modelled Residue Count: 618 
• Deposited Residue Count: 642 
• Unique protein chains: 1

2PK3

Crystal Structure of a GDP-4-keto-6-deoxy-D-mannose reductase

• PDB DOI: 10.2210/pdb2PK3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aneurinibacillus thermoaerophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-04-17 Released: 2008-03-25 
• Deposition Author(s): Webb, N.A., Garavito, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.199 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Literature

The structural basis for catalytic function of GMD and RMD, two closely related enzymes from the GDP-D-rhamnose biosynthesis pathway.

King, J.D., Poon, K.K., Webb, N.A., Anderson, E.M., McNally, D.J., Brisson, J.R., Messner, P., Garavito, R.M., Lam, J.S.

(2009) FEBS J 276: 2686-2700

• PubMed: 19459932 
• DOI: 10.1111/j.1742-4658.2009.06993.x
• Primary Citation of Related Structures:  
  2PK3


• PubMed Abstract: 
  

The rare 6-deoxysugar D-rhamnose is a component of bacterial cell surface glycans, including the D-rhamnose homopolymer produced by Pseudomonas aeruginosa, called A-band O polysaccharide. GDP-D-rhamnose synthesis from GDP-D-mannose is catalyzed by two enzymes. The first is a GDP-D-mannose-4,6-dehydratase (GMD). The second enzyme, RMD, reduces the GMD product (GDP-6-deoxy-D-lyxo-hexos-4-ulose) to GDP-d-rhamnose. Genes encoding GMD and RMD are present in P. aeruginosa, and genetic evidence indicates they act in A-band O-polysaccharide biosynthesis. Details of their enzyme functions have not, however, been previously elucidated. We aimed to characterize these enzymes biochemically, and to determine the structure of RMD to better understand what determines substrate specificity and catalytic activity in these enzymes. We used capillary electrophoresis and NMR analysis of reaction products to precisely define P. aeruginosa GMD and RMD functions. P. aeruginosa GMD is bifunctional, and can catalyze both GDP-d-mannose 4,6-dehydration and the subsequent reduction reaction to produce GDP-D-rhamnose. RMD catalyzes the stereospecific reduction of GDP-6-deoxy-D-lyxo-hexos-4-ulose, as predicted. Reconstitution of GDP-D-rhamnose biosynthesis in vitro revealed that the P. aeruginosa pathway may be regulated by feedback inhibition in the cell. We determined the structure of RMD from Aneurinibacillus thermoaerophilus at 1.8 A resolution. The structure of A. thermoaerophilus RMD is remarkably similar to that of P. aeruginosa GMD, which explains why P. aeruginosa GMD is also able to catalyze the RMD reaction. Comparison of the active sites and amino acid sequences suggests that a conserved amino acid side chain (Arg185 in P. aeruginosa GMD) may be crucial for orienting substrate and cofactor in GMD enzymes.

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Organizational Affiliation: 

Department of Molecular and Cellular Biology, University of Guelph, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-6-deoxy-D-lyxo-4-hexulose reductase	A, B	321	Aneurinibacillus thermoaerophilus	Mutation(s): 0  Gene Names: rmd EC: 1.1.1.281
UniProt
Find proteins for Q6T1X6 (Aneurinibacillus thermoaerophilus) Explore Q6T1X6  Go to UniProtKB:  Q6T1X6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A2R	C [auth A], E [auth B]	[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE C15 H24 N5 O17 P3 ICNHOLCERMYLRZ-KEOHHSTQSA-N
GDD	D [auth A], F [auth B]	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE C16 H25 N5 O16 P2 MVMSCBBUIHUTGJ-GDJBGNAASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.199 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.882	α = 72.54
b = 55.744	β = 82.95
c = 79.244	γ = 75.61

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MrBUMP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-04-17 
• Released Date: 2008-03-25 
Deposition Author(s): Webb, N.A., Garavito, R.M.

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance