1LRT

CRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE: STRUCTURAL CHARACTERIZATION OF NAD+ SITE IN MICROBIAL ENZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a ternary complex of Tritrichomonas foetus inosine 5'-monophosphate dehydrogenase: NAD+ orients the active site loop for catalysis

Gan, L.Petsko, G.A.Hedstrom, L.

(2003) Biochemistry 41: 13309-13317


  • PubMed Abstract: 
  • Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the conversion of IMP to XMP with the reduction of NAD(+), which is the rate-limiting step in the biosynthesis of guanine nucleotides. IMPDH is a promising target for chemotherapy. Microbial IM ...

    Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the conversion of IMP to XMP with the reduction of NAD(+), which is the rate-limiting step in the biosynthesis of guanine nucleotides. IMPDH is a promising target for chemotherapy. Microbial IMPDHs differ from mammalian enzymes in their lower affinity for inhibitors such as mycophenolic acid (MPA) and thiazole-4-carboxamide adenine dinucleotide (TAD). Part of this resistance is determined by the coupling between nicotinamide and adenosine subsites in the NAD(+) binding site that is postulated to involve an active site flap. To understand the structural basis of the drug selectivity, we solved the X-ray crystal structure of the catalytic core domain of Tritrichomonas foetus IMPDH in complex with IMP and beta-methylene-TAD at 2.2 A resolution. Unlike previous structures of this enzyme, the active site loop is ordered in this complex, and the catalytic Cys319 is 3.6 A from IMP, in the same plane as the hypoxanthine ring. The active site loop forms hydrogen bonds to the carboxamide of beta-Me-TAD which suggests that NAD(+) promotes the nucleophillic attack of Cys319 on IMP. The interactions of the adenosine end of TAD are very different from those in the human enzyme, suggesting the NAD(+) site may be an exploitable target for the design of antimicrobial drugs. In addition, a new K(+) site is observed at the subunit interface. This site is adjacent to beta-Me-TAD, consistent with the link between the K(+) activation and NAD(+). However, contrary to the coupling model, the flap does not cover the adenosine subsite and remains largely disordered.


    Organizational Affiliation

    Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
A, B, C, D
376Tritrichomonas foetusGene Names: IMPDH
EC: 1.1.1.205
Find proteins for P50097 (Tritrichomonas foetus)
Go to UniProtKB:  P50097
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
IMP
Query on IMP

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Download CCD File 
A, B, C, D
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
TAD
Query on TAD

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Download CCD File 
A, B, C, D
BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE DINUCLEOTIDE
C20 H27 N7 O13 P2 S
CRWWKLKZKYLFQV-HVIRUEHBSA-N
 Ligand Interaction
TRS
Query on TRS

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Download CCD File 
A, B, C, D
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
BOG
Query on BOG

Download SDF File 
Download CCD File 
A
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TADKi: 2300 nM BINDINGMOAD
TADKi: 2300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 96.144α = 90.00
b = 112.369β = 90.00
c = 161.997γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-07
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-26
    Type: Refinement description, Source and taxonomy