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PDBsum entry 1h1z

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protein ligands metals Protein-protein interface(s) links
Isomerase PDB id
1h1z
Jmol
Contents
Protein chains
220 a.a. *
Ligands
SO4 ×2
Metals
_ZN ×2
* Residue conservation analysis
PDB id:
1h1z
Name: Isomerase
Title: The structure of the cytosolic d-ribulose-5-phosphate 3-epimerase from rice complexed with sulfate and zinc
Structure: D-ribulose-5-phosphate 3-epimerase. Chain: a, b. Engineered: yes
Source: Oryza sativa. Rice. Organism_taxid: 4530. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
3.4Å     R-factor:   0.202     R-free:   0.256
Authors: S.Jelakovic,G.E.Schulz
Key ref:
S.Jelakovic et al. (2003). Structure and catalytic mechanism of the cytosolic D-ribulose-5-phosphate 3-epimerase from rice. J Mol Biol, 326, 127-135. PubMed id: 12547196 DOI: 10.1016/S0022-2836(02)01374-8
Date:
25-Jul-02     Release date:   30-Jan-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9SE42  (RPE1_ORYSJ) -  Ribulose-phosphate 3-epimerase, cytoplasmic isoform
Seq:
Struc:
228 a.a.
220 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!
  Cellular component     plasma membrane   3 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/S0022-2836(02)01374-8 J Mol Biol 326:127-135 (2003)
PubMed id: 12547196  
 
 
Structure and catalytic mechanism of the cytosolic D-ribulose-5-phosphate 3-epimerase from rice.
S.Jelakovic, S.Kopriva, K.H.Süss, G.E.Schulz.
 
  ABSTRACT  
 
Cytosolic D-ribulose-5-phosphate 3-epimerase from rice was crystallized after EDTA treatment and structurally elucidated by X-ray diffraction to 1.9A resolution. A prominent Zn(2+) site at the active center was established in a soaking experiment. The structure was compared with that of the EDTA-treated crystalline enzyme from the chloroplasts of potato plant leaves showing some structural differences, in particular the "closed" state of a strongly conserved mobile loop covering the substrate at its putative binding site. The previous proposal for the active center was confirmed and the most likely substrate binding position and conformation was derived from the locations of the bound zinc and sulfate ions and of three water molecules. Assuming that the bound zinc ion is an integral part of the enzyme, a reaction mechanism involving a well-stabilized cis-enediolate intermediate is suggested.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The catalyzed reaction of Image -ribulose-5-phosphate 3-epimerase.
Figure 8.
Figure 8. Stereo view of the active center with a Ru5P model. All depicted residues are strongly conserved (Figure 5). Some interactions are shown as dotted lines. The substrate model has the CNS-refined conformation that is close to the water-fitted conformation shown in Figure 7. Note the three methionine residues shielding one side of Zn2+ and also Phe150 of the strongly conserved mobile loop b6-a6 that points to the solvent but is likely to close as a lid over the bound substrate.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 326, 127-135) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19524482 R.Hänsch, and R.R.Mendel (2009).
Physiological functions of mineral micronutrients (Cu, Zn, Mn, Fe, Ni, Mo, B, Cl).
  Curr Opin Plant Biol, 12, 259-266.  
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.  
15632186 K.Savolainen, P.Bhaumik, W.Schmitz, T.J.Kotti, E.Conzelmann, R.K.Wierenga, and J.K.Hiltunen (2005).
Alpha-methylacyl-CoA racemase from Mycobacterium tuberculosis. Mutational and structural characterization of the active site and the fold.
  J Biol Chem, 280, 12611-12620.
PDB code: 1x74
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
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