3R5H

Crystal Structure of ADP-AIR complex of purK: N5-carboxyaminoimidazole ribonucleotide synthetase

• PDB DOI: https://doi.org/10.2210/pdb3R5H/pdb

• Classification: LYASE
• Organism(s): Bacillus anthracis str. A0248
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-18 Released: 2012-03-21 
• Deposition Author(s): Fung, L.W., Tuntland, M.L., Santarsiero, B.D., Johnson, M.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Elucidation of the bicarbonate binding site and insights into the carboxylation mechanism of (N(5))-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis

Tuntland, M.L., Santarsiero, B.D., Johnson, M.E., Fung, L.W.

(2014) Acta Crystallogr D Biol Crystallogr 70: 3057-3065

• PubMed: 25372694 
• DOI: https://doi.org/10.1107/S1399004714021166
• Primary Citation of Related Structures:  
  3QFF, 3R5H, 3V4S, 4DLK


• PubMed Abstract: 
  

  Structures of (N(5))-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis with various combinations of ATP, ADP, Mg(2+), bicarbonate and aminoimidazole ribonucleotide (AIR) in the active site are presented. The binding site of bicarbonate has only been speculated upon previously, but is shown here for the first time. The binding involves interactions with the conserved residues Arg272, His274 and Lys348. These structures provide insights into each ligand in the active site and allow a possible mechanism to be proposed for the reaction that converts bicarbonate and AIR, in the presence of ATP, to produce (N(5))-carboxyaminoimidazole ribonucleotide. The formation of a carboxyphosphate intermediate through ATP phosphoryl transfer is proposed, followed by carboxylation of AIR to give the product, facilitated by a cluster of conserved residues and an active-site water network.

---

Organizational Affiliation: 

Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 87.91 kDa 
• Atom Count: 6,576 
• Modelled Residue Count: 760 
• Deposited Residue Count: 778 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole carboxylase, ATPase subunit	A, B	389	Bacillus anthracis str. A0248	Mutation(s): 0  Gene Names: BAA_0344, purK EC: 4.1.1.21

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
AIR	D [auth A], G [auth B]	5-AMINOIMIDAZOLE RIBONUCLEOTIDE C8 H14 N3 O7 P PDACUKOKVHBVHJ-XVFCMESISA-N
MG	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.442	α = 90
b = 82.785	β = 90
c = 168.233	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Fung, L.W., Tuntland, M.L., Santarsiero, B.D., Johnson, M.E.

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2015-03-18
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description