PDBsum entry: 2fwi

Lyase

PDB id: 2fwi

Contents

Protein chains

159 a.a. *

Ligands

AIR

Waters ×285

* Residue conservation analysis

PDB id:

2fwi

Name:

Lyase

Title:

Structure of pure (n5-carboxyaminoimidazole ribonucleotide mutase) h59d, from the acidophilic bacterium acetobacter aceti, complexed with 5-aminoimidazole ribonucleotide (air)

Structure:

N5-carboxyaminoimidazole ribonucleotide mutase. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Acetobacter aceti. Organism_taxid: 435. Strain: 1023. Gene: pure. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Octamer (from PDB file)

Resolution:

1.94Å R-factor: 0.165 R-free: 0.191

Authors:

C.M.Starks,T.J.Kappock

Key ref:

C.Z.Constantine et al. (2006). Biochemical and structural studies of N5-carboxyaminoimidazole ribonucleotide mutase from the acidophilic bacterium Acetobacter aceti. Biochemistry, 45, 8193-8208. PubMed id: 16819818 DOI: 10.1021/bi060465n

Date:

02-Feb-06 Release date: 13-Jun-06

Protein chains

Q2QJL3  (Q2QJL3_ACEAC) -  N5-carboxyaminoimidazole ribonucleotide mutase

Seq: 182 a.a.

Struc: 159 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 = 5-amino-1-(5-phospho-D- ribosyl)imidazole-4-carboxylate

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

 Gene Ontology (GO) functional annotation 

• Biological process: purine nucleotide biosynthetic process (2 terms)
• Biochemical function: isomerase activity (3 terms)

Added reference

DOI no: 10.1021/bi060465n

Biochemistry 45:8193-8208 (2006)

PubMed id: 16819818

Biochemical and structural studies of N5-carboxyaminoimidazole ribonucleotide mutase from the acidophilic bacterium Acetobacter aceti.

C.Z.Constantine, C.M.Starks, C.P.Mill, A.E.Ransome, S.J.Karpowicz, J.A.Francois, R.A.Goodman, T.J.Kappock.

ABSTRACT

N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) mutase (PurE) catalyzes the reversible interconversion of acid-labile compounds N5-CAIR and 4-carboxy-5-aminoimidazole ribonucleotide (CAIR). We have examined PurE from the acidophilic bacterium Acetobacter aceti (AaPurE), focusing on its adaptation to acid pH and the roles of conserved residues His59 and His89. Both AaPurE and Escherichia coli PurE showed quasi-reversible acid-mediated inactivation, but wt AaPurE was much more stable at pH 3.5, with a > or = 20 degrees C higher thermal unfolding temperature at all pHs. His89 is not essential and does not function as part of a proton relay system. The kcat pH-rate profile was consistent with the assignment of pK1 to unproductive protonation of bound nucleotide and pK2 to deprotonation of His59. A 1.85 A resolution crystal structure of the inactive mutant H59N-AaPurE soaked in CAIR showed that protonation of CAIR C4 can occur in the absence of His59. The resulting species, modeled as isoCAIR [4(R)-carboxy-5-iminoimidazoline ribonucleotide], is strongly stabilized by extensive interactions with the enzyme and a water molecule. The carboxylate moiety is positioned in a small pocket proposed to facilitate nucleotide decarboxylation in the forward direction (N5-CAIR --> CAIR) [Meyer, E., Kappock, T. J., Osuji, C., and Stubbe, J. (1999) Biochemistry 38, 3012-3018]. Comparisons with model studies suggest that in the reverse (nonbiosynthetic) direction PurE favors protonation of CAIR C4. We suggest that the essential role of protonated His59 is to lower the barrier to decarboxylation by stabilizing a CO2-azaenolate intermediate.