2ATE

Structure of the complex of PurE with NitroAIR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1021/bi602436g
  • Primary Citation of Related Structures:  
  • Also Cited By: 5CLJ, 5CLG

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoribosylaminoimidazole carboxylase catalytic subunit
A
169Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: purE
EC: 5.4.99.18
Find proteins for P0AG18 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG18
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NIA
Query on NIA

Download SDF File 
Download CCD File 
A
((2R,3S,4R,5R)-5-(5-AMINO-4-NITRO-1H-IMIDAZOL-1-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE
4-NITRO-5-AMINOIMIDAZOLE RIBONUCLEOTIDE; NITRO AIR
C8 H13 N4 O9 P
YVRCVGZPIYHJLU-AFCXAGJDSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NIAKd: 86 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.149 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 112.495α = 90.00
b = 112.495β = 90.00
c = 49.796γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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