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PDBsum entry 1nxm

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protein Protein-protein interface(s) links
Isomerase PDB id
1nxm
Jmol
Contents
Protein chains
194 a.a. *
Waters ×633
* Residue conservation analysis
PDB id:
1nxm
Name: Isomerase
Title: The high resolution structures of rmlc from streptococcus suis
Structure: Dtdp-6-deoxy-d-xylo-4-hexulose 3,5-epimerase. Chain: a, b. Synonym: dtdp-4-dehydrorhamnose 3,5-epimerase. Engineered: yes
Source: Streptococcus suis. Organism_taxid: 1307. Strain: serotype 2. Gene: rmlc. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
1.30Å     R-factor:   0.145     R-free:   0.174
Authors: C.Dong,L.L.Major,A.Allen,W.Blankenfeldt,D.Maskell, J.H.Naismith
Key ref:
C.Dong et al. (2003). High-resolution structures of RmlC from Streptococcus suis in complex with substrate analogs locate the active site of this class of enzyme. Structure, 11, 715-723. PubMed id: 12791259 DOI: 10.1016/S0969-2126(03)00098-4
Date:
11-Feb-03     Release date:   24-Jun-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8GIQ0  (Q8GIQ0_STRSU) -  DTDP-4-dehydrorhamnose 3,5-epimerase
Seq:
Struc:
197 a.a.
194 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.1.3.13  - dTDP-4-dehydrorhamnose 3,5-epimerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
6-Deoxyhexose Biosynthesis
      Reaction: dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
= dTDP-4-dehydro-beta-L-rhamnose
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     lipopolysaccharide biosynthetic process   1 term 
  Biochemical function     isomerase activity     2 terms  

 

 
    Key reference    
 
 
DOI no: 10.1016/S0969-2126(03)00098-4 Structure 11:715-723 (2003)
PubMed id: 12791259  
 
 
High-resolution structures of RmlC from Streptococcus suis in complex with substrate analogs locate the active site of this class of enzyme.
C.Dong, L.L.Major, A.Allen, W.Blankenfeldt, D.Maskell, J.H.Naismith.
 
  ABSTRACT  
 
Nature achieves the epimerization of carbohydrates by a variety of chemical routes. One common route is that performed by the class of enzyme defined by dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase (RmlC) from the rhamnose pathway. Earlier studies failed to identify the key residues in catalysis. We report the 1.3 A structure of RmlC from Streptococcus suis type 2 and its complexes with dTDP-D-glucose and dTDP-D-xylose. The streptococcal RmlC enzymes belong to a separate subgroup, sharing only 25% identity with RmlC from other bacteria, yet the S. suis enzyme has similar kinetic properties and structure to other RmlC enzymes. Structure, sequence alignment, and mutational analysis have now allowed reliable identification of the catalytic residues and their roles.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The Sequential Steps in the Conversion of dTDP-6-Deoxy-D-Xylo-4-Hexulose to dTDP-6-Deoxy-L-Lyxo-4-Hexulose by RmlC, as Conventionally WrittenOur data do not define the order of epimerization, and therefore the choice of C5 first is arbitrary. dTMP represents deoxythymidine monophosphate. The substrate mimics used in this study, dTDP-D-glucose and dTDP-D-xylose, are shown.
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 715-723) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19478949 G.Agarwal, M.Rajavel, B.Gopal, and N.Srinivasan (2009).
Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold.
  PLoS One, 4, e5736.  
18425854 M.Tello, M.Rejzek, B.Wilkinson, D.M.Lawson, and R.A.Field (2008).
Tyl1a, a TDP-6-deoxy-D-xylo-4-hexulose 3,4-isomerase from Streptomyces fradiae: structure prediction, mutagenesis and solvent isotope incorporation experiments to investigate reaction mechanism.
  Chembiochem, 9, 1295-1302.  
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
16514445 M.Tello, P.Jakimowicz, J.C.Errey, C.L.Freel Meyers, C.T.Walsh, M.J.Buttner, D.M.Lawson, and R.A.Field (2006).
Characterisation of Streptomyces spheroides NovW and revision of its functional assignment to a dTDP-6-deoxy-D-xylo-4-hexulose 3-epimerase.
  Chem Commun (Camb), (), 1079-1081.  
16411240 P.Jakimowicz, M.Tello, C.L.Meyers, C.T.Walsh, M.J.Buttner, R.A.Field, and D.M.Lawson (2006).
The 1.6-A resolution crystal structure of NovW: a 4-keto-6-deoxy sugar epimerase from the novobiocin biosynthetic gene cluster of Streptomyces spheroides.
  Proteins, 63, 261-265.
PDB code: 2c0z
16077096 A.Teplyakov, G.Obmolova, J.Toedt, M.Y.Galperin, and G.L.Gilliland (2005).
Crystal structure of the bacterial YhcH protein indicates a role in sialic acid catabolism.
  J Bacteriol, 187, 5520-5527.
PDB code: 1s4c
15608122 C.Z.Zhou, P.Meyer, S.Quevillon-Cheruel, I.L.De La Sierra-Gallay, B.Collinet, M.Graille, K.Blondeau, J.M.François, N.Leulliot, I.Sorel, A.Poupon, J.Janin, and H.Van Tilbeurgh (2005).
Crystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new sequence family of the jelly-roll fold.
  Protein Sci, 14, 209-215.
PDB codes: 1xe7 1xe8
15159413 A.B.Merkel, L.L.Major, J.C.Errey, M.D.Burkart, R.A.Field, C.T.Walsh, and J.H.Naismith (2004).
The position of a key tyrosine in dTDP-4-Keto-6-deoxy-D-glucose-5-epimerase (EvaD) alters the substrate profile for this RmlC-like enzyme.
  J Biol Chem, 279, 32684-32691.
PDB code: 1oi6
12876368 P.Jakimowicz, C.L.Freel Meyers, C.T.Walsh, M.J.Buttner, and D.M.Lawson (2003).
Crystallization and preliminary X-ray studies on the putative dTDP sugar epimerase NovW from the novobiocin biosynthetic cluster of Streptomyces spheroides.
  Acta Crystallogr D Biol Crystallogr, 59, 1507-1509.  
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.