1RM0

Crystal Structure of Myo-Inositol 1-Phosphate Synthase From Saccharomyces cerevisiae In Complex With NAD+ and 2-deoxy-D-glucitol 6-(E)-vinylhomophosphonate

• PDB DOI: https://doi.org/10.2210/pdb1RM0/pdb

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


• Deposited: 2003-11-26 Released: 2004-05-25 
• Deposition Author(s): Jin, X., Foley, K.M., Geiger, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.244 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 

Literature

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.

Jin, X., Foley, K.M., Geiger, J.H.

(2004) J Biol Chem 279: 13889-13895

• PubMed: 14684747 
• DOI: https://doi.org/10.1074/jbc.M308986200
• Primary Citation of Related Structures:  
  1RM0


• PubMed Abstract: 
  

  1l-myo-inositol 1-phosphate (MIP) synthase catalyzes the conversion of d-glucose 6-phosphate to 1l-myo-inositol 1-phosphate, the first and rate-limiting step in the biosynthesis of all inositol-containing compounds. It involves an oxidation, enolization, intramolecular aldol cyclization, and reduction. Here we present the structure of MIP synthase in complex with NAD(+) and a high-affinity inhibitor, 2-deoxy-d-glucitol 6-(E)-vinylhomophosphonate. This structure reveals interactions between the enzyme active site residues and the inhibitor that are significantly different from that proposed for 2-deoxy-d-glucitol 6-phosphate in the previously published structure of MIP synthase-NAD(+)-2-deoxy-d-glucitol 6-phosphate. There are several other conformational changes in NAD(+) and the enzyme active site as well. Based on the new structural data, we propose a new and completely different mechanism for MIP synthase.

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Organizational Affiliation: 

Michigan State University, Chemistry Department, 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: 121.04 kDa 
• Atom Count: 8,687 
• Modelled Residue Count: 1,041 
• Deposited Residue Count: 1,066 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
myo-inositol-phosphate synthase	A, B	533	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: INO1 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], F [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
D6P	D [auth A]	(3,4,5,7-TETRAHYDROXY-HEPT-1-ENYL)-PHOSPHONIC ACID C7 H15 O7 P CZQSGBWQBMZTMQ-AEVYZNAZSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
D6P	Binding MOAD:  1RM0	Ki: 670 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.244 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.81	α = 90
b = 97.78	β = 126.3
c = 122.29	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-25 
Deposition Author(s): Jin, X., Foley, K.M., Geiger, J.H.

Revision History  

• Version 1.0: 2004-05-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations