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PDBsum entry 1rpx

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protein ligands Protein-protein interface(s) links
3-epimerase PDB id
1rpx
Jmol
Contents
Protein chains
230 a.a. *
Ligands
SO4 ×3
Waters ×177
* Residue conservation analysis
PDB id:
1rpx
Name: 3-epimerase
Title: D-ribulose-5-phosphate 3-epimerase from solanum tuberosum ch
Structure: Protein (ribulose-phosphate 3-epimerase). Chain: a, b, c. Engineered: yes
Source: Solanum tuberosum. Potato. Organism_taxid: 4113. Organelle: chloroplast. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PDB file)
Resolution:
2.30Å     R-factor:   0.174     R-free:   0.212
Authors: J.Kopp,G.E.Schulz
Key ref:
J.Kopp et al. (1999). Structure and mechanism of the amphibolic enzyme D-ribulose-5-phosphate 3-epimerase from potato chloroplasts. J Mol Biol, 287, 761-771. PubMed id: 10191144 DOI: 10.1006/jmbi.1999.2643
Date:
01-Dec-98     Release date:   07-Apr-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q43843  (RPE_SOLTU) -  Ribulose-phosphate 3-epimerase, chloroplastic (Fragment)
Seq:
Struc:
280 a.a.
230 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.1.3.1  - Ribulose-phosphate 3-epimerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-ribulose 5-phosphate = D-xylulose 5-phosphate
D-ribulose 5-phosphate
= D-xylulose 5-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.1999.2643 J Mol Biol 287:761-771 (1999)
PubMed id: 10191144  
 
 
Structure and mechanism of the amphibolic enzyme D-ribulose-5-phosphate 3-epimerase from potato chloroplasts.
J.Kopp, S.Kopriva, K.H.Süss, G.E.Schulz.
 
  ABSTRACT  
 
Ribulose-5-phosphate 3-epimerase (EC 5.1.3.1) catalyzes the interconversion of ribulose-5-phosphate and xylulose-5-phosphate in the Calvin cycle and in the oxidative pentose phosphate pathway. The enzyme from potato chloroplasts was expressed in Escherichia coli, isolated and crystallized. The crystal structure was elucidated by multiple isomorphous replacement and refined at 2.3 A resolution. The enzyme is a homohexamer with D3 symmetry. The subunit chain fold is a (beta alpha)8-barrel. A sequence comparison with homologous epimerases outlined the active center and indicated that all members of this family are likely to share the same catalytic mechanism. The substrate could be modeled by putting its phosphate onto the observed sulfate position and its epimerized C3 atom between two carboxylates that participate in an extensive hydrogen bonding system. A mutation confirmed the crucial role of one of these carboxylates. The geometry together with the conservation pattern suggests that the negative charge of the putative cis-ene-diolate intermediate is stabilized by the transient induced dipoles of a methionine sulfur "cushion", which is proton-free and therefore prevents isomerization instead of epimerization.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Stereoview of the β-barrel (strands β8 and β1 are transparent) with the most prominent active center residues, showing the location of the central water molecule and the two rows of hydrogen-bonded residues within the (βα)[8]-barrel. The strongly conserved, mobile loop β6-α6 is depicted at the top.
Figure 9.
Figure 9. Proposed protonation scheme of the hydrogen bonding network around the central water molecule of the active center. Substrate atoms C2, O2, C3 and O3 are sketched at their modeled position. In the proposed initial protonation state (black), Asp43 is charged. The first reaction step converts Ru5P (black) to the cis-ene-diolate intermediate (red). The second step continues the reaction to Xu5P (blue). We suggest that the intermediate oxyanion is stabilized by induced, favorably oriented dipoles formed by the soft sulfur electron shells.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 287, 761-771) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18849419 R.Shi, M.Pineda, E.Ajamian, Q.Cui, A.Matte, and M.Cygler (2008).
Structure of L-xylulose-5-Phosphate 3-epimerase (UlaE) from the anaerobic L-ascorbate utilization pathway of Escherichia coli: identification of a novel phosphate binding motif within a TIM barrel fold.
  J Bacteriol, 190, 8137-8144.
PDB codes: 3cqh 3cqi 3cqj 3cqk
18063718 F.R.Tabita, T.E.Hanson, H.Li, S.Satagopan, J.Singh, and S.Chan (2007).
Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs.
  Microbiol Mol Biol Rev, 71, 576-599.
PDB code: 2qyg
17163439 C.Marchand, P.Le Maréchal, Y.Meyer, and P.Decottignies (2006).
Comparative proteomic approaches for the isolation of proteins interacting with thioredoxin.
  Proteomics, 6, 6528-6537.  
16304640 J.Caruthers, J.Bosch, F.Buckner, W.Van Voorhis, P.Myler, E.Worthey, C.Mehlin, E.Boni, G.DeTitta, J.Luft, A.Lauricella, O.Kalyuzhniy, L.Anderson, F.Zucker, M.Soltis, and W.G.Hol (2006).
Structure of a ribulose 5-phosphate 3-epimerase from Plasmodium falciparum.
  Proteins, 62, 338-342.
PDB code: 1tqx
17001104 K.Au, N.S.Berrow, E.Blagova, I.W.Boucher, M.P.Boyle, J.A.Brannigan, L.G.Carter, T.Dierks, G.Folkers, R.Grenha, K.Harlos, R.Kaptein, A.K.Kalliomaa, V.M.Levdikov, C.Meier, N.Milioti, O.Moroz, A.Müller, R.J.Owens, N.Rzechorzek, S.Sainsbury, D.I.Stuart, T.S.Walter, D.G.Waterman, A.J.Wilkinson, K.S.Wilson, N.Zaccai, R.M.Esnouf, and M.J.Fogg (2006).
Application of high-throughput technologies to a structural proteomics-type analysis of Bacillus anthracis.
  Acta Crystallogr D Biol Crystallogr, 62, 1267-1275.  
15333955 E.L.Wise, J.Akana, J.A.Gerlt, and I.Rayment (2004).
Structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 A resolution.
  Acta Crystallogr D Biol Crystallogr, 60, 1687-1690.
PDB code: 1tqj
15340924 K.B.Murray, W.R.Taylor, and J.M.Thornton (2004).
Toward the detection and validation of repeats in protein structure.
  Proteins, 57, 365-380.  
11395407 J.A.Gerlt, and P.C.Babbitt (2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
  Annu Rev Biochem, 70, 209-246.  
11114506 M.F.Giraud, and J.H.Naismith (2000).
The rhamnose pathway.
  Curr Opin Struct Biol, 10, 687-696.  
10625676 S.Kopriva, A.Koprivova, and K.H.Süss (2000).
Identification, cloning, and properties of cytosolic D-ribulose-5-phosphate 3-epimerase from higher plants.
  J Biol Chem, 275, 1294-1299.  
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.