Crystal structure of Medicago truncatula Histidinol-Phosphate Phosphatase (MtHPP) in complex with L-histidinol

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 

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Structural Studies of Medicago truncatula Histidinol Phosphate Phosphatase from Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants.

Ruszkowski, M.Dauter, Z.

(2016) J Biol Chem 291: 9960-9973

  • DOI: https://doi.org/10.1074/jbc.M115.708727
  • Primary Citation of Related Structures:  
    5EQ7, 5EQ8, 5EQ9, 5EQA

  • PubMed Abstract: 

    The penultimate enzyme in the histidine biosynthetic pathway catalyzes dephosphorylation of l-histidinol 1-phosphate (HOLP) into l-histidinol. The recently discovered in Arabidopsis thaliana plant-type histidinol phosphate phosphatase (HPP) shares no homology with the two other HPP superfamilies known previously in prokaryotes and resembles myo-inositol monophosphatases (IMPases). In this work, identification of an HPP enzyme from a model legume, Medicago truncatula (MtHPP) was based on the highest sequence identity to A. thaliana enzyme. Biochemical assays confirmed that MtHPP was able to cleave inorganic phosphate from HOLP but not from d-myo-inositol-1-phosphate, the main substrate of IMPases. Dimers of MtHPP, determined by size exclusion chromatography, in the presence of CO2 or formaldehyde form mutual, methylene-bridged cross-links between Lys(158) and Cys(245) residues. Four high resolution crystal structures, namely complexes with HOLP (substrate), l-histidinol (product), and PO4 (3-) (by-product) as well as the structure showing the cross-linking between two MtHPP molecules, provide detailed structural information on the enzyme. Based on the crystal structures, the enzymatic reaction mechanism of IMPases is accustomed to fit the data for MtHPP. The enzymatic reaction, which requires Mg(2+) cations, is catalyzed mainly by amino acid residues from the N-terminal domain. The C-terminal domain, sharing little identity with IMPases, is responsible for the substrate specificity (i.e. allows the enzyme to distinguish between HOLP and d-myo-inositol-1-phosphate). Structural features, mainly the presence of a conserved Asp(246), allow MtHPP to bind HOLP specifically.

  • Organizational Affiliation

    From the Synchrotron Radiation Research Section of MCL, NCI, National Institutes of Health, Argonne, Illinois 60439 mruszkowski@anl.gov.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol monophosphatase277Medicago truncatulaMutation(s): 0 
Gene Names: MTR_3g117220
Find proteins for G7J7Q5 (Medicago truncatula)
Explore G7J7Q5 
Go to UniProtKB:  G7J7Q5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7J7Q5
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MLZ
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.296α = 90
b = 87.296β = 90
c = 61.747γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references