PDBsum entry 3k5h

Lyase

PDB id: 3k5h

Contents

Protein chains

382 a.a. *

Ligands

ATP ×4

Metals

_MG ×8

Waters ×849

* Residue conservation analysis

PDB id:

3k5h

Name:

Lyase

Title:

Crystal structure of carboxyaminoimidazole ribonucleotide synthase from asperigillus clavatus complexed with atp

Structure:

Phosphoribosyl-aminoimidazole carboxylase. Chain: a, b, c, d. Fragment: residues 1-383. Engineered: yes

Source:

Aspergillus clavatus. Organism_taxid: 5057. Strain: nrrl 1. Gene: acla_051590, ade2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.198 R-free: 0.261

Authors:

J.B.Thoden,H.M.Holden,H.Paritala,S.M.Firestine

Key ref:

J.B.Thoden et al. (2010). Structural and functional studies of Aspergillus clavatus N(5)-carboxyaminoimidazole ribonucleotide synthetase . Biochemistry, 49, 752-760. PubMed id: 20050602

Date:

07-Oct-09 Release date: 20-Oct-09

Protein chains

A1CII2  (A1CII2_ASPCL) -  Phosphoribosylaminoimidazole carboxylase from Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1 / QM 1276 / 107)

Seq: 572 a.a.

Struc: 382 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.1.21 - phosphoribosylaminoimidazole carboxylase.
• Pathway: Purine Biosynthesis (late stages)
• Reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + H⁺ = 5-amino- 1-(5-phospho-beta-D-ribosyl)imidazole + CO2

5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate (Bound ligand (Het Group name = ATP) matches with 60.61% similarity) + H(+) = 5-amino- 1-(5-phospho-beta-D-ribosyl)imidazole + CO2

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

Added reference

Biochemistry 49:752-760 (2010)

PubMed id: 20050602

Structural and functional studies of Aspergillus clavatus N(5)-carboxyaminoimidazole ribonucleotide synthetase .

J.B.Thoden, H.M.Holden, H.Paritala, S.M.Firestine.

ABSTRACT

N(5)-Carboxyaminoimidazole ribonucleotide synthetase (N(5)-CAIR synthetase), a key enzyme in microbial de novo purine biosynthesis, catalyzes the conversion of aminoimidazole ribonucleotide (AIR) to N(5)-CAIR. To date, this enzyme has been observed only in microorganisms, and thus, it represents an ideal target for antimicrobial drug development. Here we report the cloning, crystallization, and three-dimensional structural analysis of Aspergillus clavatus N(5)-CAIR synthetase solved in the presence of either Mg(2)ATP or MgADP and AIR. These structures, determined to 2.1 and 2.0 A, respectively, revealed that AIR binds in a pocket analogous to that observed for other ATP-grasp enzymes involved in purine metabolism. On the basis of these models, a site-directed mutagenesis study was subsequently conducted that focused on five amino acid residues located in the active site region of the enzyme. These investigations demonstrated that Asp 153 and Lys 353 play critical roles in catalysis without affecting substrate binding. All other mutations affected substrate binding and, in some instances, catalysis as well. Taken together, the structural and kinetic data presented here suggest a catalytic mechanism whereby Mg(2)ATP and bicarbonate first react to form the unstable intermediate carboxyphosphate. This intermediate subsequently decarboxylates to CO(2) and inorganic phosphate, and the amino group of AIR, through general base assistance by Asp 153, attacks CO(2) to form N(5)-CAIR.