Myo-inositol phosphate synthase mIPS from A. fulgidus

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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Reaching for Mechanistic Consensus Across Life Kingdoms: Structure and Insights into Catalysis of the myo-Inositol-1-phosphate Synthase (mIPS) from Archaeoglobus fulgidus

Stieglitz, K.A.Yang, H.Roberts, M.F.Stec, B.

(2005) Biochemistry 44: 213-224

  • DOI: https://doi.org/10.1021/bi048267o
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    myo-Inositol-1-phosphate synthase (mIPS) catalyzes the first step in the synthesis of l-myo-inositol-1-phosphate. We have solved and refined the structure of the mIPS from the hyperthermophilic sulfate reducer Archaeoglobus fulgidus at 1.9 A resolution. The enzyme crystallized from poly(ethylene glycol) in the P1 space group with one tetramer in the asymmetric unit and provided a view of the entire biologically active oligomer. Despite significant changes in sequence length and amino acid composition, the general architecture of the archaeal enzyme is similar to that of the eukaryotic mIPS from Saccharomyces cerevisiae and bacterial mIPS from Mycobacterium tuberculosis. The enhanced thermostability of the archaeal enzyme as compared to that from yeast is consistent with deletion of a number of surface loops that results in a significantly smaller protein. In the structure of the A. fulgidus mIPS, the active sites of all four subunits were fully ordered and contained NAD(+) and inorganic phosphate. The structure also contained a single metal ion (identified as K(+)) in two of the four subunits. The analysis of the electrostatic potential maps of the protein suggested the presence of a second metal-ion-binding site in close proximity to the first metal ion and NAD(+). The modeling of the substrate and known inhibitors suggests a critical role for the second metal ion in catalysis and provides insights into the common elements of the catalytic cycle in enzymes from different life kingdoms.

  • Organizational Affiliation

    Department of Chemistry, University of Texas at El Paso, El Paso, Texas 79968, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
myo-inositol-1-phosphate synthase
A, B, C, D
392Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Find proteins for O28480 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O28480 
Go to UniProtKB:  O28480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO28480
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
N [auth D]
C21 H27 N7 O14 P2
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
J [auth C],
M [auth D]
O4 P
Query on K

Download Ideal Coordinates CCD File 
H [auth B],
K [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.77α = 65.79
b = 83.94β = 72.43
c = 91.79γ = 74.98
Software Package:
Software NamePurpose
X-PLORmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description