3TSD

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

PDB DOI: https://doi.org/10.2210/pdb3TSD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus anthracis str. Ames
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-09-13 Released: 2011-10-05
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.245
R-Value Work: 0.192
R-Value Observed: 0.195

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 22788966 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 111.34 kDa
Atom Count: 6,667
Modelled Residue Count: 868
Deposited Residue Count: 1,022
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B	511	Bacillus anthracis str. Ames	Mutation(s): 0 Gene Names: guaB, BAS0011, BA_0008, GBAA_0008 EC: 1.1.1.205
UniProt
Find proteins for A0A6L8P2U9 (Bacillus anthracis) Explore A0A6L8P2U9 Go to UniProtKB: A0A6L8P2U9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6L8P2U9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XMP Query on XMP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	XANTHOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₄ O₉ P DCTLYFZHFGENCW-UUOKFMHZSA-O		Interactions Focus chain C [auth A] Focus chain D [auth B]
TAR Query on TAR Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain E [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
XMP	PDBBind: 3TSD	Ki: 2.18e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
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 = 123.25	α = 90
b = 123.25	β = 90
c = 141.636	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-10-05

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

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