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PDBsum entry 1db3

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protein links
Lyase PDB id
1db3
Jmol
Contents
Protein chain
335 a.a. *
Waters ×113
* Residue conservation analysis
PDB id:
1db3
Name: Lyase
Title: E.Coli gdp-mannose 4,6-dehydratase
Structure: Gdp-mannose 4,6-dehydratase. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PDB file)
Resolution:
2.30Å     R-factor:   0.205     R-free:   0.232
Authors: J.R.Somoza,S.Menon,W.S.Somers,F.X.Sullivan
Key ref:
J.R.Somoza et al. (2000). Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose. Structure, 8, 123-135. PubMed id: 10673432 DOI: 10.1016/S0969-2126(00)00088-5
Date:
02-Nov-99     Release date:   24-Nov-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0AC88  (GM4D_ECOLI) -  GDP-mannose 4,6-dehydratase
Seq:
Struc:
373 a.a.
335 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.47  - GDP-mannose 4,6-dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
GDP-L-Fucose and GDP-mannose Biosynthesis
      Reaction: GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H2O
GDP-mannose
= GDP-4-dehydro-6-deoxy-D-mannose
+ H(2)O
      Cofactor: NAD(+)
NAD(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     cellular metabolic process   4 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(00)00088-5 Structure 8:123-135 (2000)
PubMed id: 10673432  
 
 
Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose.
J.R.Somoza, S.Menon, H.Schmidt, D.Joseph-McCarthy, A.Dessen, M.L.Stahl, W.S.Somers, F.X.Sullivan.
 
  ABSTRACT  
 
Background: GDP-mannose 4,6 dehydratase (GMD) catalyzes the conversion of GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose. This is the first and regulatory step in the de novo biosynthesis of GDP-(L)-fucose. Fucose forms part of a number of glycoconjugates, including the ABO blood groups and the selectin ligand sialyl Lewis X. Defects in GDP-fucose metabolism have been linked to leukocyte adhesion deficiency type II (LADII). Results: The structure of the GDP-mannose 4,6 dehydratase apo enzyme has been determined and refined using data to 2.3 A resolution. GMD is a homodimeric protein with each monomer composed of two domains. The larger N-terminal domain binds the NADP(H) cofactor in a classical Rossmann fold and the C-terminal domain harbors the sugar-nucleotide binding site. We have determined the GMD dissociation constants for NADP, NADPH and GDP-mannose. Each GMD monomer binds one cofactor and one substrate molecule, suggesting that both subunits are catalytically competent. GDP-fucose acts as a competitive inhibitor, suggesting that it binds to the same site as GDP-mannose, providing a mechanism for the feedback inhibition of fucose biosynthesis. Conclusions: The X-ray structure of GMD reveals that it is a member of the short-chain dehydrogenase/reductase (SDR) family of proteins. We have modeled the binding of NADP and GDP-mannose to the enzyme and mutated four of the active-site residues to determine their function. The combined modeling and mutagenesis data suggests that at position 133 threonine substitutes serine as part of the serine-tyrosine-lysine catalytic triad common to the SDR family and Glu 135 functions as an active-site base.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. GDP-fucose biosynthesis. NADP bound to GMD is reduced and then oxidized during the course of the reaction. GFS catalyzes two distinct reactions: the epimerization of the GDP-4-keto, 6-deoxymannose at C3 and C5 followed by the subsequent reduction at C4 to yield GDP-fucose.
 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 123-135) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19459932 J.D.King, K.K.Poon, N.A.Webb, E.M.Anderson, D.J.McNally, J.R.Brisson, P.Messner, R.M.Garavito, and J.S.Lam (2009).
The structural basis for catalytic function of GMD and RMD, two closely related enzymes from the GDP-D-rhamnose biosynthesis pathway.
  FEBS J, 276, 2686-2700.
PDB code: 2pk3
19126547 Y.L.Chen, Y.H.Chen, Y.C.Lin, K.C.Tsai, and H.T.Chiu (2009).
Functional characterization and substrate specificity of spinosyn rhamnosyltransferase by in vitro reconstitution of spinosyn biosynthetic enzymes.
  J Biol Chem, 284, 7352-7363.  
18422615 B.Liu, Y.A.Knirel, L.Feng, A.V.Perepelov, S.N.Senchenkova, Q.Wang, P.R.Reeves, and L.Wang (2008).
Structure and genetics of Shigella O antigens.
  FEMS Microbiol Rev, 32, 627-653.  
17974560 F.Fruscione, L.Sturla, G.Duncan, J.L.Van Etten, P.Valbuzzi, A.De Flora, E.Di Zanni, and M.Tonetti (2008).
Differential role of NADP+ and NADPH in the activity and structure of GDP-D-mannose 4,6-dehydratase from two chlorella viruses.
  J Biol Chem, 283, 184-193.  
17135259 B.D.Barrows, S.M.Haslam, L.J.Bischof, H.R.Morris, A.Dell, and R.V.Aroian (2007).
Resistance to Bacillus thuringiensis toxin in Caenorhabditis elegans from loss of fucose.
  J Biol Chem, 282, 3302-3311.  
17190829 T.Oka, T.Nemoto, and Y.Jigami (2007).
Functional analysis of Arabidopsis thaliana RHM2/MUM4, a multidomain protein involved in UDP-D-glucose to UDP-L-rhamnose conversion.
  J Biol Chem, 282, 5389-5403.  
16650000 S.Rhomberg, C.Fuchsluger, D.Rendić, K.Paschinger, V.Jantsch, P.Kosma, and I.B.Wilson (2006).
Reconstitution in vitro of the GDP-fucose biosynthetic pathways of Caenorhabditis elegans and Drosophila melanogaster.
  FEBS J, 273, 2244-2256.  
15805590 N.M.Koropatkin, and H.M.Holden (2005).
Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi complexed with CDP-D-xylose.
  Acta Crystallogr D Biol Crystallogr, 61, 365-373.
PDB code: 1wvg
15016358 A.C.Price, Y.M.Zhang, C.O.Rock, and S.W.White (2004).
Cofactor-induced conformational rearrangements establish a catalytically competent active site and a proton relay conduit in FabG.
  Structure, 12, 417-428.
PDB codes: 1q7b 1q7c
14739333 N.A.Webb, A.M.Mulichak, J.S.Lam, H.L.Rocchetta, and R.M.Garavito (2004).
Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a bacterial GDP-D-rhamnose biosynthetic pathway.
  Protein Sci, 13, 529-539.
PDB code: 1rpn
12954627 B.A.Wolucka, and M.Van Montagu (2003).
GDP-mannose 3',5'-epimerase forms GDP-L-gulose, a putative intermediate for the de novo biosynthesis of vitamin C in plants.
  J Biol Chem, 278, 47483-47490.  
12642575 N.M.Koropatkin, H.W.Liu, and H.M.Holden (2003).
High resolution x-ray structure of tyvelose epimerase from Salmonella typhi.
  J Biol Chem, 278, 20874-20881.
PDB code: 1orr
12045109 X.M.He, and H.W.Liu (2002).
Formation of unusual sugars: mechanistic studies and biosynthetic applications.
  Annu Rev Biochem, 71, 701-754.  
11752432 B.A.Wolucka, G.Persiau, J.Van Doorsselaere, M.W.Davey, H.Demol, J.Vandekerckhove, M.Van Montagu, M.Zabeau, and W.Boerjan (2001).
Partial purification and identification of GDP-mannose 3",5"-epimerase of Arabidopsis thaliana, a key enzyme of the plant vitamin C pathway.
  Proc Natl Acad Sci U S A, 98, 14843-14848.  
11114506 M.F.Giraud, and J.H.Naismith (2000).
The rhamnose pathway.
  Curr Opin Struct Biol, 10, 687-696.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.