PDBsum entry 2nsh

Lyase

PDB id: 2nsh

Contents

Protein chain

163 a.a. *

Ligands

NIA

Waters ×123

* Residue conservation analysis

PDB id:

2nsh

Name:

Lyase

Title:

E. Coli pure h45q mutant complexed with nitro-air

Structure:

Phosphoribosylaminoimidazole carboxylase catalytic subunit. Chain: a. Synonym: air carboxylase, airc. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: pure. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.80Å R-factor: 0.178 R-free: 0.211

Authors:

S.E.Ealick,M.Morar

Key ref:

A.A.Hoskins et al. (2007). N5-CAIR mutase: role of a CO2 binding site and substrate movement in catalysis. Biochemistry, 46, 2842-2855. PubMed id: 17298082 DOI: 10.1021/bi602436g

Date:

04-Nov-06 Release date: 24-Apr-07

Protein chain

P0AG18  (PURE_ECOLI) -  N5-carboxyaminoimidazole ribonucleotide mutase from Escherichia coli (strain K12)

Seq: 169 a.a.

Struc: 163 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.5.4.99.18 - 5-(carboxyamino)imidazole ribonucleotide mutase.
• Reaction: 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole + H⁺ = 5-amino-1- (5-phospho-D-ribosyl)imidazole-4-carboxylate

5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole (Bound ligand (Het Group name = NIA) matches with 76.00% similarity) + H(+) = 5-amino-1- (5-phospho-D-ribosyl)imidazole-4-carboxylate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/bi602436g

Biochemistry 46:2842-2855 (2007)

PubMed id: 17298082

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

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

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.