Crystal Structure of Inosine-5'-monophosphate Dehydrogenase from Bacillus anthracis str. Ames complexed with XMP

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

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Bacillus anthracis inosine 5'-monophosphate dehydrogenase in action: the first bacterial series of structures of phosphate ion-, substrate-, and product-bound complexes.

Makowska-Grzyska, M.Kim, Y.Wu, R.Wilton, R.Gollapalli, D.R.Wang, X.K.Zhang, R.Jedrzejczak, R.Mack, J.C.Maltseva, N.Mulligan, R.Binkowski, T.A.Gornicki, P.Kuhn, M.L.Anderson, W.F.Hedstrom, L.Joachimiak, A.

(2012) Biochemistry 51: 6148-6163

  • DOI: https://doi.org/10.1021/bi300511w
  • Primary Citation of Related Structures:  
    3TSB, 3TSD, 3USB

  • PubMed Abstract: 

    Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the first unique step of the GMP branch of the purine nucleotide biosynthetic pathway. This enzyme is found in organisms of all three kingdoms. IMPDH inhibitors have broad clinical applications in cancer treatment, as antiviral drugs and as immunosuppressants, and have also displayed antibiotic activity. We have determined three crystal structures of Bacillus anthracis IMPDH, in a phosphate ion-bound (termed "apo") form and in complex with its substrate, inosine 5'-monophosphate (IMP), and product, xanthosine 5'-monophosphate (XMP). This is the first example of a bacterial IMPDH in more than one state from the same organism. Furthermore, for the first time for a prokaryotic enzyme, the entire active site flap, containing the conserved Arg-Tyr dyad, is clearly visible in the structure of the apoenzyme. Kinetic parameters for the enzymatic reaction were also determined, and the inhibitory effect of XMP and mycophenolic acid (MPA) has been studied. In addition, the inhibitory potential of two known Cryptosporidium parvum IMPDH inhibitors was examined for the B. anthracis enzyme and compared with those of three bacterial IMPDHs from Campylobacter jejuni, Clostridium perfringens, and Vibrio cholerae. The structures contribute to the characterization of the active site and design of inhibitors that specifically target B. anthracis and other microbial IMPDH enzymes.

  • Organizational Affiliation

    Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase
A, B
511Bacillus anthracis str. AmesMutation(s): 0 
Gene Names: guaBBAS0011BA_0008GBAA_0008
Find proteins for A0A6L8P2U9 (Bacillus anthracis)
Explore A0A6L8P2U9 
Go to UniProtKB:  A0A6L8P2U9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6L8P2U9
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
XMP PDBBind:  3TSD Ki: 2.18e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: I 4
  • Diffraction Data: https://doi.org/10.18430/M33TSD
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.25α = 90
b = 123.25β = 90
c = 141.636γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
PHENIXmodel building
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2013-04-10
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description