1JKI | pdb_00001jki

myo-Inositol-1-phosphate Synthase Complexed with an Inhibitor, 2-deoxy-glucitol-6-phosphate

• PDB DOI: https://doi.org/10.2210/pdb1JKI/pdb

• Classification: ISOMERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-07-12 Released: 2002-04-10 
• Deposition Author(s): Stein, A.J., Geiger, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.280 (Depositor) 
• R-Value Work: 
  0.208 (Depositor) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

The crystal structure and mechanism of 1-L-myo-inositol- 1-phosphate synthase

Stein, A.J., Geiger, J.H.

(2002) J Biological Chem 277: 9484-9491

• PubMed: 11779862 
• DOI: https://doi.org/10.1074/jbc.M109371200
• Primary Citation Related Structures: 
  1JKF, 1JKI


• PubMed Abstract: 
  

  1-l-myo-Inositol-1-phosphate synthase catalyzes the conversion of d-glucose 6-phosphate to 1-l-myo-inositol-1-phosphate (MIP), the first and rate-limiting step in the biosynthesis of all inositol-containing compounds. It involves an oxidation, intramolecular aldol cyclization, and reduction. We have determined the first crystal structure of MIP synthase. We present structures of both the NAD-bound enzyme and the enzyme bound to an inhibitor, 2-deoxy-glucitol-6-phosphate. While 58 amino acids are disordered in the unbound form of the enzyme in the vicinity of the active site, the inhibitor nucleates the folding of this domain in a striking example of induced fit, serving to completely encapsulate it within the enzyme. Three helices and a long beta-strand are formed in this process. We postulate a mechanism for the conversion based on the structure of the inhibitor-bound complex.

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Organizational Affiliation: 
• Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 121.27 kDa 
• Atom Count: 9,006 
• Modeled Residue Count: 1,049 
• Deposited Residue Count: 1,066 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
myo-inositol-1-phosphate synthase	A, B	533	Saccharomyces cerevisiae	Mutation(s): 0  EC: 5.5.1.4
UniProt
Find proteins for P11986 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P11986  Go to UniProtKB:  P11986

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	E [auth A], H [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
DG6	D [auth A], G [auth B]	2-DEOXY-GLUCITOL-6-PHOSPHATE C6 H15 O8 P KLPBNGZTTQNYHR-PBXRRBTRSA-N
NH4	C [auth A], F [auth B]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.280 (Depositor) 
• R-Value Work:  0.208 (Depositor) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.728	α = 90
b = 98.309	β = 126.093
c = 121.855	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-04-10 
Deposition Author(s): Stein, A.J., Geiger, J.H.

Revision History  

• Version 1.0: 2002-04-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description