Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 18.37 kDa 
• Atom Count: 1373 
• Modelled Residue Count: 162 
• Deposited Residue Count: 169 
• Unique protein chains: 1

2ATE

Structure of the complex of PurE with NitroAIR

• PDB DOI: 10.2210/pdb2ATE/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-08-24 Released: 2006-08-29 
• Deposition Author(s): Kappock, T.J., Mathews, I.I., Zaugg, J.B., Peng, P., Hoskins, A.A., Okamoto, A., Ealick, S.E., Stubbe, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.202 
• R-Value Work: 0.149 
• R-Value Observed: 0.152 

Literature

N5-CAIR mutase: role of a CO2 binding site and substrate movement in catalysis.

Hoskins, A.A., Morar, M., Kappock, T.J., Mathews, I.I., Zaugg, J.B., Barder, T.E., Peng, P., Okamoto, A., Ealick, S.E., Stubbe, J.

(2007) Biochemistry 46: 2842-2855

• PubMed: 17298082 
• DOI: 10.1021/bi602436g
• Primary Citation of Related Structures:  
  2ATE, 2NSH, 2NSJ, 2NSL


• PubMed Abstract: 
  

N5-Carboxyaminoimidazole ribonucleotide mutase (N5-CAIR mutase or PurE) from Escherichia coli catalyzes the reversible interconversion of N5-CAIR to carboxyaminoimidazole ribonucleotide (CAIR) with direct CO2 transfer. Site-directed mutagenesis, a pH-rate profile, DFT calculations, and X-ray crystallography together provide new insight into the mechanism of this unusual transformation. These studies suggest that a conserved, protonated histidine (His45) plays an essential role in catalysis. The importance of proton transfers is supported by DFT calculations on CAIR and N5-CAIR analogues in which the ribose 5'-phosphate is replaced with a methyl group. The calculations suggest that the nonaromatic tautomer of CAIR (isoCAIR) is only 3.1 kcal/mol higher in energy than its aromatic counterpart, implicating this species as a potential intermediate in the PurE-catalyzed reaction. A structure of wild-type PurE cocrystallized with 4-nitroaminoimidazole ribonucleotide (NO2-AIR, a CAIR analogue) and structures of H45N and H45Q PurEs soaked with CAIR have been determined and provide the first insight into the binding of an intact PurE substrate. A comparison of 19 available structures of PurE and PurE mutants in apo and nucleotide-bound forms reveals a common, buried carboxylate or CO2 binding site for CAIR and N5-CAIR in a hydrophobic pocket in which the carboxylate or CO2 interacts with backbone amides. This work has led to a mechanistic proposal in which the carboxylate orients the substrate for proton transfer from His45 to N5-CAIR to form an enzyme-bound aminoimidazole ribonucleotide (AIR) and CO2 intermediate. Subsequent movement of the aminoimidazole moiety of AIR reorients it for addition of CO2 at C4 to generate isoCAIR. His45 is now in a position to remove a C4 proton to produce CAIR.

---

Related Citations: 

• Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway.
  Mathews, I.I., Kappock, T.J., Stubbe, J., Ealick, S.
  (1999) Structure 7: 1395

• Modular evolution of the purine biosynthetic pathway.
  Kappock, T.J., Ealick, S.E., Stubbe, J.
  (2000) Curr Opin Chem Biol 4: 567

---

Organizational Affiliation: 

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole carboxylase catalytic subunit	A	169	Escherichia coli	Mutation(s): 4  Gene Names: purE EC: 4.1.1.21 (PDB Primary Data), 5.4.99.18 (UniProt)
UniProt
Find proteins for P0AG18 (Escherichia coli (strain K12)) Explore P0AG18  Go to UniProtKB:  P0AG18

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NIA	B [auth A]	((2R,3S,4R,5R)-5-(5-AMINO-4-NITRO-1H-IMIDAZOL-1-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE C8 H13 N4 O9 P YVRCVGZPIYHJLU-AFCXAGJDSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Binding Affinity Annotations
ID	Source	Binding Affinity
NIA	PDBBind:  2ATE	Kd: 86 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.202 
• R-Value Work: 0.149 
• R-Value Observed: 0.152 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.495	α = 90
b = 112.495	β = 90
c = 49.796	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-24 
• Released Date: 2006-08-29 
Deposition Author(s): Kappock, T.J., Mathews, I.I., Zaugg, J.B., Peng, P., Hoskins, A.A., Okamoto, A., Ealick, S.E., Stubbe, J.

Revision History  

• Version 1.0: 2006-08-29
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance