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Lyase PDB id
1kew
Jmol
Contents
Protein chains
361 a.a. *
Ligands
TYD ×2
NAD ×2
GOL ×3
Waters ×701
* Residue conservation analysis
PDB id:
1kew
Name: Lyase
Title: The crystal structure of dtdp-d-glucose 4,6-dehydratase (rml salmonella enterica serovar typhimurium with thymidine diph bound
Structure: Dtdp-d-glucose 4,6-dehydratase. Chain: a, b. Synonym: dtdp-glucose 4,6-dehydratase. Rmlb. Engineered: yes
Source: Salmonella enterica subsp. Enterica se typhimurium. Organism_taxid: 90371. Strain: subsp. Enterica serovar typhimurium. Gene: rmlb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.205     R-free:   0.221
Authors: S.T.M.Allard,K.Beis,M.-F.Giraud,A.D.Hegeman,J.W.Gross,C.Whit M.Graninger,P.Messner,A.G.Allen,J.H.Naismith
Key ref:
S.T.Allard et al. (2002). Toward a structural understanding of the dehydratase mechanism. Structure, 10, 81-92. PubMed id: 11796113 DOI: 10.1016/S0969-2126(01)00694-3
Date:
17-Nov-01     Release date:   25-Jan-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P26391  (RMLB_SALTY) -  dTDP-glucose 4,6-dehydratase
Seq:
Struc: 		361 a.a.
361 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.46  - dTDP-glucose 4,6-dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		6-Deoxyhexose Biosynthesis
      Reaction: dTDP-glucose = dTDP-4-dehydro-6-deoxy-D-glucose + H2O
dTDP-glucose
 = dTDP-4-dehydro-6-deoxy-D-glucose
 + H(2)O
      Cofactor: NAD(+)
NAD(+)
Bound ligand (Het Group name = NAD) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cellular metabolic process   4 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(01)00694-3 Structure 10:81-92 (2002)
PubMed id: 11796113  
 
 
Toward a structural understanding of the dehydratase mechanism.
S.T.Allard, K.Beis, M.F.Giraud, A.D.Hegeman, J.W.Gross, R.C.Wilmouth, C.Whitfield, M.Graninger, P.Messner, A.G.Allen, D.J.Maskell, J.H.Naismith.
 
  ABSTRACT  
 
dTDP-D-glucose 4,6-dehydratase (RmlB) was first identified in the L-rhamnose biosynthetic pathway, where it catalyzes the conversion of dTDP-D-glucose into dTDP-4-keto-6-deoxy-D-glucose. The structures of RmlB from Salmonella enterica serovar Typhimurium in complex with substrate deoxythymidine 5'-diphospho-D-glucose (dTDP-D-glucose) and deoxythymidine 5'-diphosphate (dTDP), and RmlB from Streptococcus suis serotype 2 in complex with dTDP-D-glucose, dTDP, and deoxythymidine 5'-diphospho-D-pyrano-xylose (dTDP-xylose) have all been solved at resolutions between 1.8 A and 2.4 A. The structures show that the active sites are highly conserved. Importantly, the structures show that the active site tyrosine functions directly as the active site base, and an aspartic and glutamic acid pairing accomplishes the dehydration step of the enzyme mechanism. We conclude that the substrate is required to move within the active site to complete the catalytic cycle and that this movement is driven by the elimination of water. The results provide insight into members of the SDR superfamily.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. The Mechanism of dTDP-D-Glucose 4,6-Dehydratase (RmlB)The catalytic process can be divided into three steps: oxidation, dehydration, and reduction. Oxidation: NAD^+ extracts a hydride from the C4 position of the glucose ring and the active site tyrosine removes a proton from the glucosyl C4'-hydroxyl group. Dehydration: the concerted removal of water across glucosyl C5 and C6. The active site glutamic acid deprotonates C5 and the aspartic acid protonates the leaving C6'-hydroxyl group. Reduction: the pyranose ring moves within the active site, allowing the active site tyrosine to protonate glucosyl C5, and NADH returns the hydride to glucosyl C6.
 
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 81-92) copyright 2002.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20538863 M.Parakkottil Chothi, G.A.Duncan, A.Armirotti, C.Abergel, J.R.Gurnon, J.L.Van Etten, C.Bernardi, G.Damonte, and M.Tonetti (2010).
Identification of an L-rhamnose synthetic pathway in two nucleocytoplasmic large DNA viruses.
  J Virol, 84, 8829-8838.  
20162627 O.Doppelt-Azeroual, F.Delfaud, F.Moriaud, and A.G.de Brevern (2010).
Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins.
  Protein Sci, 19, 847-867.  
  19058170 C.J.Thibodeaux, C.E.Melançon, and H.W.Liu (2008).
Natural-product sugar biosynthesis and enzymatic glycodiversification.
  Angew Chem Int Ed Engl, 47, 9814-9859.  
17893902 D.J.McNally, I.C.Schoenhofen, R.S.Houliston, N.H.Khieu, D.M.Whitfield, S.M.Logan, H.C.Jarrell, and J.R.Brisson (2008).
CMP-pseudaminic acid is a natural potent inhibitor of PseB, the first enzyme of the pseudaminic acid pathway in Campylobacter jejuni and Helicobacter pylori.
  ChemMedChem, 3, 55-59.  
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.  
19011750 K.L.Kavanagh, H.Jörnvall, B.Persson, and U.Oppermann (2008).
Medium- and short-chain dehydrogenase/reductase gene and protein families : the SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes.
  Cell Mol Life Sci, 65, 3895-3906.  
18291320 P.Kallio, Z.Liu, P.Mäntsälä, J.Niemi, and M.Metsä-Ketelä (2008).
Sequential action of two flavoenzymes, PgaE and PgaM, in angucycline biosynthesis: chemoenzymatic synthesis of gaudimycin C.
  Chem Biol, 15, 157-166.  
17046787 C.Dong, L.L.Major, V.Srikannathasan, J.C.Errey, M.F.Giraud, J.S.Lam, M.Graninger, P.Messner, M.R.McNeil, R.A.Field, C.Whitfield, and J.H.Naismith (2007).
RmlC, a C3' and C5' carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation.
  J Mol Biol, 365, 146-159.
PDB codes: 2ixc 2ixh 2ixi 2ixj 2ixk 2ixl
17654627 K.Palmu, K.Ishida, P.Mäntsälä, C.Hertweck, and M.Metsä-Ketelä (2007).
Artificial reconstruction of two cryptic angucycline antibiotic biosynthetic pathways.
  Chembiochem, 8, 1577-1584.  
17031886 D.J.McNally, I.C.Schoenhofen, E.F.Mulrooney, D.M.Whitfield, E.Vinogradov, J.S.Lam, S.M.Logan, and J.R.Brisson (2006).
Identification of labile UDP-ketosugars in Helicobacter pylori, Campylobacter jejuni and Pseudomonas aeruginosa: key metabolites used to make glycan virulence factors.
  Chembiochem, 7, 1865-1868.  
16286454 I.C.Schoenhofen, D.J.McNally, E.Vinogradov, D.Whitfield, N.M.Young, S.Dick, W.W.Wakarchuk, J.R.Brisson, and S.M.Logan (2006).
Functional characterization of dehydratase/aminotransferase pairs from Helicobacter and Campylobacter: enzymes distinguishing the pseudaminic acid and bacillosamine biosynthetic pathways.
  J Biol Chem, 281, 723-732.  
16936924 J.H.Naismith (2006).
Inferring the chemical mechanism from structures of enzymes.
  Chem Soc Rev, 35, 763-770.  
17087520 N.B.Olivier, M.M.Chen, J.R.Behr, and B.Imperiali (2006).
In vitro biosynthesis of UDP-N,N'-diacetylbacillosamine by enzymes of the Campylobacter jejuni general protein glycosylation system.
  Biochemistry, 45, 13659-13669.  
16495121 V.L.Yip, and S.G.Withers (2006).
Breakdown of oligosaccharides by the process of elimination.
  Curr Opin Chem Biol, 10, 147-155.  
15809294 G.J.Williams, S.D.Breazeale, C.R.Raetz, and J.H.Naismith (2005).
Structure and function of both domains of ArnA, a dual function decarboxylase and a formyltransferase, involved in 4-amino-4-deoxy-L-arabinose biosynthesis.
  J Biol Chem, 280, 23000-23008.
PDB codes: 2bll 2bln
15750655 L.Ballell, R.J.Young, and R.A.Field (2005).
Synthesis and evaluation of mimetics of UDP and UDP-alpha-D-galactose, dTDP and dTDP-alpha-D-glucose with monosaccharides replacing the key pyrophosphate unit.
  Org Biomol Chem, 3, 1109-1115.  
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
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
15341727 S.S.Rajan, X.Yang, F.Collart, V.L.Yip, S.G.Withers, A.Varrot, J.Thompson, G.J.Davies, and W.F.Anderson (2004).
Novel catalytic mechanism of glycoside hydrolysis based on the structure of an NAD+/Mn2+ -dependent phospho-alpha-glucosidase from Bacillus subtilis.
  Structure, 12, 1619-1629.
PDB code: 1u8x
14570895 S.T.Allard, W.W.Cleland, and H.M.Holden (2004).
High resolution X-ray structure of dTDP-glucose 4,6-dehydratase from Streptomyces venezuelae.
  J Biol Chem, 279, 2211-2220.
PDB codes: 1r66 1r6d
12077451 A.B.Merkel, G.K.Temple, M.D.Burkart, H.C.Losey, K.Beis, C.T.Walsh, and J.H.Naismith (2002).
Purification, crystallization and preliminary structural studies of dTDP-4-keto-6-deoxy-glucose-5-epimerase (EvaD) from Amycolatopsis orientalis, the fourth enzyme in the dTDP-L-epivancosamine biosynthetic pathway.
  Acta Crystallogr D Biol Crystallogr, 58, 1226-1228.
PDB code: 1ofn
12171937 J.Sivaraman, V.Sauvé, A.Matte, and M.Cygler (2002).
Crystal structure of Escherichia coli glucose-1-phosphate thymidylyltransferase (RffH) complexed with dTTP and Mg2+.
  J Biol Chem, 277, 44214-44219.
PDB code: 1mc3
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 codes are shown on the right.