1AK5 | pdb_00001ak5

INOSINE MONOPHOSPHATE DEHYDROGENASE (IMPDH) FROM TRITRICHOMONAS FOETUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.265 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.218 (Depositor) 
  • R-Value Observed: 
    0.218 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of Tritrichomonas foetus inosine-5'-monophosphate dehydrogenase and the enzyme-product complex.

Whitby, F.G.Luecke, H.Kuhn, P.Somoza, J.R.Huete-Perez, J.A.Phillips, J.D.Hill, C.P.Fletterick, R.J.Wang, C.C.

(1997) Biochemistry 36: 10666-10674

  • DOI: https://doi.org/10.1021/bi9708850
  • Primary Citation Related Structures: 
    1AK5

  • PubMed Abstract: 

    Inosine-5'-monophosphate dehydrogenase (IMPDH) is an attractive drug target for the control of parasitic infections. The enzyme catalyzes the oxidation of inosine monophosphate (IMP) to xanthosine monophosphate (XMP), the committed step in de novo guanosine monophosphate (GMP) biosynthesis. We have determined the crystal structures of IMPDH from the protozoan parasite Tritrichomonas foetus in the apo form at 2.3 A resolution and the enzyme-XMP complex at 2.6 A resolution. Each monomer of this tetrameric enzyme is comprised of two domains, the largest of which includes an eight-stranded parallel beta/alpha-barrel that contains the enzyme active site at the C termini of the barrel beta-strands. A second domain, comprised of residues 102-220, is disordered in the crystal. IMPDH is expected to be active as a tetramer, since the active site cavity is formed by strands from adjacent subunits. An intrasubunit disulfide bond, seen in the crystal structure, may stabilize the protein in a less active form, as high concentrations of reducing agent have been shown to increase enzyme activity. Disorder at the active site suggests that a high degree of flexibility may be inherent in the catalytic function of IMPDH. Unlike IMPDH from other species, the T. foetus enzyme has a single arginine that is largely responsible for coordinating the substrate phosphate in the active site. This structural uniqueness may facilitate structure-based identification and design of compounds that specifically inhibit the parasite enzyme.


  • Organizational Affiliation
    • Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, 94143-0446, USA. frankw@solitude.med.utah.edu

Macromolecule Content 

  • Total Structure Weight: 55.64 kDa 
  • Atom Count: 2,582 
  • Modeled Residue Count: 329 
  • Deposited Residue Count: 503 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE503Tritrichomonas suisMutation(s): 0 
EC: 1.1.1.205
UniProt
Find proteins for P50097 (Tritrichomonas foetus)
Explore P50097 
Go to UniProtKB:  P50097
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50097
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.265 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.218 (Depositor) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.25α = 90
b = 157.25β = 90
c = 157.25γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
ROTAVATA/AGROVATAdata reduction
PHASESphasing
XTALVIEWrefinement
X-PLORrefinement
CCP4data scaling
ROTAVATAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 1997-09-17 
  • Deposition Author(s): Whitby, F.G.

Revision History  (Full details and data files)

  • Version 1.0: 1997-09-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary