3ORS

Crystal Structure of N5-Carboxyaminoimidazole Ribonucleotide Mutase from Staphylococcus aureus

• PDB DOI:  https://doi.org/10.2210/pdb3ORS/pdb

• Classification: ISOMERASE,BIOSYNTHETIC PROTEIN
• Organism(s): Staphylococcus aureus subsp. aureus str. Newman
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-09-07 Released: 2011-07-20 
• Deposition Author(s): Brugarolas, P., Duguid, E.M., Zhang, W., Poor, C.B., He, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.203 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

Structural and biochemical characterization of N5-carboxyaminoimidazole ribonucleotide synthetase and N5-carboxyaminoimidazole ribonucleotide mutase from Staphylococcus aureus.

Brugarolas, P., Duguid, E.M., Zhang, W., Poor, C.B., He, C.

(2011) Acta Crystallogr D Biol Crystallogr 67: 707-715

• PubMed: 21795812 
• DOI: https://doi.org/10.1107/S0907444911023821
• Primary Citation of Related Structures:  
  3ORQ, 3ORR, 3ORS


• PubMed Abstract: 
  

With the rapid rise of methicillin-resistant Staphylococcus aureus infections, new strategies against S. aureus are urgently needed. De novo purine biosynthesis is a promising yet unexploited target, insofar as abundant evidence has shown that bacteria with compromised purine biosynthesis are attenuated. Fundamental differences exist within the process by which humans and bacteria convert 5-aminoimidazole ribonucleotide (AIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR). In bacteria, this transformation occurs through a two-step conversion catalyzed by PurK and PurE; in humans, it is mediated by a one-step conversion catalyzed by class II PurE. Thus, these bacterial enzymes are potential targets for selective antibiotic development. Here, the first comprehensive structural and biochemical characterization of PurK and PurE from S. aureus is presented. Structural analysis of S. aureus PurK reveals a nonconserved phenylalanine near the AIR-binding site that occupies the putative position of the imidazole ring of AIR. Mutation of this phenylalanine to isoleucine or tryptophan reduced the enzyme efficiency by around tenfold. The K(m) for bicarbonate was determined for the first time for a PurK enzyme and was found to be ∼18.8 mM. The structure of PurE is described in comparison to that of human class II PurE. It is confirmed biochemically that His38 is essential for function. These studies aim to provide foundations for future structure-based drug-discovery efforts against S. aureus purine biosynthesis.

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Organizational Affiliation: 

Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, GCIS E321, Chicago, IL 60637, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 140.58 kDa 
• Atom Count: 10,788 
• Modelled Residue Count: 1,286 
• Deposited Residue Count: 1,304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N5-Carboxyaminoimidazole Ribonucleotide Mutase	A, B, C, D, E, F, G, H	163	Staphylococcus aureus subsp. aureus str. Newman	Mutation(s): 0  Gene Names: NWMN_0933, purE, CNH35_05340 EC: 5.4.99.18
UniProt
Find proteins for A0A0H3K7Y1 (Staphylococcus aureus (strain Newman)) Explore A0A0H3K7Y1  Go to UniProtKB:  A0A0H3K7Y1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth B], O [auth C], P [auth C], Q [auth D], R [auth D], S [auth D], T [auth D], U [auth E], V [auth F], W [auth F], X [auth G], Y [auth G], Z [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.203 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.302	α = 90
b = 78.207	β = 113.94
c = 93.039	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Brugarolas, P., Duguid, E.M., Zhang, W., Poor, C.B., He, C.

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2012-03-28
  Changes: Database references
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description