2NSL

E. coli PurE H45N mutant complexed with CAIR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

N(5)-CAIR Mutase: Role of a CO(2) 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.


    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): 1 
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
C2R
Query on C2R

Download SDF File 
Download CCD File 
A
5-AMINO-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1H-IMIDAZOLE-4-CARBOXYLIC ACID
CAIR, 4-CARBOXY-5-AMINOIMIDAZOLE RIBONUCLEOTIDE
C9 H14 N3 O9 P
XFVULMDJZXYMSG-ZIYNGMLESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C2RKd: 20900 nM BINDINGMOAD
C2RKd: 20900 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 111.317α = 90.00
b = 111.317β = 90.00
c = 49.200γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance