1ME7

Inosine Monophosphate Dehydrogenase (IMPDH) From Tritrichomonas Foetus with RVP and MOA bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Tritrichomonas foetus Inosine Monophosphate Dehydrogenase in Complex with the Inhibitor Ribavirin Monophosphate Reveals a Catalysis-dependent Ion-binding Site

Prosise, G.L.Wu, J.Luecke, H.

(2002) J.Biol.Chem. 277: 50654-50659

  • DOI: 10.1074/jbc.M208330200
  • Primary Citation of Related Structures:  1ME8

  • PubMed Abstract: 
  • Inosine monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step in GMP biosynthesis. The resulting intracellular pool of guanine nucleotides is of great importance to all cells for use in DNA and RNA synthesis, metabolism, and signal tra ...

    Inosine monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step in GMP biosynthesis. The resulting intracellular pool of guanine nucleotides is of great importance to all cells for use in DNA and RNA synthesis, metabolism, and signal transduction. The enzyme binds IMP and the cofactor NAD(+) in random order, IMP is converted to XMP, NAD(+) is reduced to NADH, and finally, NADH and then XMP are released sequentially. XMP is subsequently converted into GMP by GMP synthetase. Drugs that decrease GMP synthesis by inhibiting IMPDH have been shown to have antiproliferative as well as antiviral activity. Several drugs are in use that target the substrate- or cofactor-binding site; however, due to differences between the mammalian and microbial isoforms, most drugs are far less effective against the microbial form of the enzyme than the mammalian form. The high resolution crystal structures of the protozoan parasite Tritrichomonas foetus IMPDH complexed with the inhibitor ribavirin monophosphate as well as monophosphate together with a second inhibitor, mycophenolic acid, are presented here. These structures reveal an active site cation identified previously only in the Chinese hamster IMPDH structure with covalently bound IMP. This cation was not found previously in apo IMPDH, IMPDH in complex with XMP, or covalently bound inhibitor, indicating that the cation-binding site may be catalysis-dependent. A comparison of T. foetus IMPDH with the Chinese hamster and Streptococcus pyogenes structures reveals differences in the active site loop architecture, which contributes to differences in cation binding during the catalytic sequence and the kinetic rates between bacterial, protozoan, and mammalian enzymes. Exploitation of these differences may lead to novel inhibitors, which favor the microbial form of the enzyme.


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
A
503Tritrichomonas foetusGene Names: IMPDH
EC: 1.1.1.205
Find proteins for P50097 (Tritrichomonas foetus)
Go to UniProtKB:  P50097
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MOA
Query on MOA

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Download CCD File 
A
MYCOPHENOLIC ACID
6-(1,3-DIHYDRO-7-HYDROXY-5-METHOXY-4-METHYL-1-OXOISOBENZOFURAN-6-YL)-4-METHYL-4-HEXANOIC ACID
C17 H20 O6
HPNSFSBZBAHARI-RUDMXATFSA-N
 Ligand Interaction
RVP
Query on RVP

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Download CCD File 
A
RIBAVIRIN MONOPHOSPHATE
C8 H13 N4 O8 P
SDWIOXKHTFOULX-AFCXAGJDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RVPKi: 65 nM BINDINGMOAD
RVPKi: 65 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.233 
  • Space Group: P 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 155.068α = 90.00
b = 155.068β = 90.00
c = 155.068γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance