PDBsum entry 1p1k

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Isomerase PDB id
Jmol PyMol
Protein chains
525 a.a. *
NAI ×2
Waters ×178
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of the 1l-myo-inositol 1-phosphate synthas complexed with nadh in the presence of edta
Structure: Inositol-3-phosphate synthase. Chain: a, b. Synonym: 1l-myo-inositol 1-phosphate synthase, myo-inositol phosphate synthase, mi-1-p synthase, ips. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PDB file)
2.10Å     R-factor:   0.209     R-free:   0.261
Authors: X.Jin,J.H.Geiger
Key ref:
X.Jin and J.H.Geiger (2003). Structures of NAD(+)- and NADH-bound 1-l-myo-inositol 1-phosphate synthase. Acta Crystallogr D Biol Crystallogr, 59, 1154-1164. PubMed id: 12832758 DOI: 10.1107/S0907444903008205
12-Apr-03     Release date:   08-Jul-03    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P11986  (INO1_YEAST) -  Inositol-3-phosphate synthase
533 a.a.
525 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Inositol-3-phosphate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

myo-Inositol Biosynthesis
      Reaction: D-glucose 6-phosphate = 1D-myo-inositol 3-phosphate
D-glucose 6-phosphate
= 1D-myo-inositol 3-phosphate
      Cofactor: NAD(+)
Bound ligand (Het Group name = NAI) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     lipid metabolic process   3 terms 
  Biochemical function     isomerase activity     2 terms  


DOI no: 10.1107/S0907444903008205 Acta Crystallogr D Biol Crystallogr 59:1154-1164 (2003)
PubMed id: 12832758  
Structures of NAD(+)- and NADH-bound 1-l-myo-inositol 1-phosphate synthase.
X.Jin, J.H.Geiger.
1-l-myo-Inositol 1-phosphate synthase catalyzes the conversion of d-glucose 6-phosphate to 1-l-myo-inositol 1-phosphate, the first and rate-limiting step in the biosynthesis of all inositol-containing compounds. It involves an oxidation, an intramolecular aldol cyclization and a reduction. Here, the structure of the enzyme in its NAD(+)-bound, NADH-bound and apo forms is presented. These structures confirm that a significant portion of the active site is disordered in the absence of a small molecule, as none of the NAD(+)-bound forms of the enzyme have ordered active sites. On the other hand, the NADH-bound form contains two small molecules in the active site: a phosphate and glycerol. The entire active site is ordered in the presence of these two molecules, completely encapsulating them within the interior cavity. Significant changes in the structure of the active site are also seen, including repositioning of the nicotinamide ring and a motion of a loop region to accommodate the bound phosphate. These changes call into question the mechanism previously proposed for the enzyme. A comparison of the yeast and mycobacterial enzymes shows a surprisingly large change in the relative orientation of the catalytic and Rossmann-fold domains in the two enzymes.
  Selected figure(s)  
Figure 9.
Figure 9 Overlay of the MIP synthase-NADH complex structure in silver and the MIP synthase-NAD^+-2-deoxy-D-glucitol 6-phosphate complex structure (Stein & Geiger, 2002[Stein, A. J. & Geiger, J. H. (2002). J. Biol. Chem. 277, 9484-9491.]) in lavender. The phosphate and glycerol in the NADH-bound structure are shown in gold, 2-deoxy-D-glucitol 6-phosphate in the previous inhibitor-bound structure in cyan, side chains of the NADH-bound structure in green and side chains of the previous inhibitor-bound structure in blue.
Figure 10.
Figure 10 Overlay of the yMIP synthase-NADH complex structure (silver) and the Tb MIP synthase structure (gold); NAD^+ molecules are shown in blue for yMIP synthase and in magenta for Tb MIP synthase.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 1154-1164) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16453101 A.Chatterjee, K.G.Dastidar, S.Maitra, A.Das-Chatterjee, H.Dihazi, K.Eschrich, and A.L.Majumder (2006).
sll1981, an acetolactate synthase homologue of Synechocystis sp. PCC6803, functions as L-myo-inositol 1-phosphate synthase.
  Planta, 224, 367-379.  
15653679 K.Neelon, Y.Wang, B.Stec, and M.F.Roberts (2005).
Probing the mechanism of the Archaeoglobus fulgidus inositol-1-phosphate synthase.
  J Biol Chem, 280, 11475-11482.  
15016817 M.Majee, S.Maitra, K.G.Dastidar, S.Pattnaik, A.Chatterjee, N.C.Hait, K.P.Das, and A.L.Majumder (2004).
A novel salt-tolerant L-myo-inositol-1-phosphate synthase from Porteresia coarctata (Roxb.) Tateoka, a halophytic wild rice: molecular cloning, bacterial overexpression, characterization, and functional introgression into tobacco-conferring salt tolerance phenotype.
  J Biol Chem, 279, 28539-28552.  
14684747 X.Jin, K.M.Foley, and J.H.Geiger (2004).
The structure of the 1L-myo-inositol-1-phosphate synthase-NAD+-2-deoxy-D-glucitol 6-(E)-vinylhomophosphonate complex demands a revision of the enzyme mechanism.
  J Biol Chem, 279, 13889-13895.
PDB code: 1rm0
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