2ATE

Structure of the complex of PurE with NitroAIR

Summary for 2ATE

• Entry DOI: 10.2210/pdb2ate/pdb
• Descriptor: Phosphoribosylaminoimidazole carboxylase catalytic subunit, ((2R,3S,4R,5R)-5-(5-AMINO-4-NITRO-1H-IMIDAZOL-1-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE (3 entities in total)
• Functional Keywords: pure, nitroair complex, lyase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 18373.93

Authors

Kappock, T.J.,Mathews, I.I.,Zaugg, J.B.,Peng, P.,Hoskins, A.A.,Okamoto, A.,Ealick, S.E.,Stubbe, J. (deposition date: 2005-08-24, release date: 2006-08-29, Last modification date: 2023-11-15)

Primary citation

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.
N5-CAIR mutase: role of a CO2 binding site and substrate movement in catalysis.
Biochemistry, 46:2842-2855, 2007

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.

PubMed: 17298082
DOI: 10.1021/bi602436g

Experimental method

X-RAY DIFFRACTION (1.8 Å)