3TSD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.653 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1021/bi300511w
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inosine-5'-monophosphate dehydrogenase
A, B
511Bacillus anthracisMutation(s): 0 
Gene Names: guaB
EC: 1.1.1.205
Find proteins for A0A0J1HJU0 (Bacillus anthracis)
Go to UniProtKB:  A0A0J1HJU0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
TAR
Query on TAR

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Download CCD File 
B
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
XMP
Query on XMP

Download SDF File 
Download CCD File 
A, B
XANTHOSINE-5'-MONOPHOSPHATE
5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE
C10 H14 N4 O9 P
DCTLYFZHFGENCW-UUOKFMHZSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XMPKi: 218000 nM PDBBIND
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 123.250α = 90.00
b = 123.250β = 90.00
c = 141.636γ = 90.00
Software Package:
Software NamePurpose
HKL-3000phasing
PHENIXmodel building
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2013-04-10
    Type: Database references