1B4K

High resolution crystal structure of a MG2-dependent 5-aminolevulinic acid dehydratase

Summary for 1B4K

• Entry DOI: 10.2210/pdb1b4k/pdb
• Descriptor: PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE), SULFATE ION, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: lyase, heme biosynthesis, magnesium, levulinic acid
• Biological source: Pseudomonas aeruginosa
• Total number of polymer chains: 2
• Total formula weight: 74604.51

Authors

Frankenberg, N.,Jahn, D.,Heinz, D.W. (deposition date: 1998-12-22, release date: 1999-07-13, Last modification date: 2024-10-30)

Primary citation

Frankenberg, N.,Erskine, P.T.,Cooper, J.B.,Shoolingin-Jordan, P.M.,Jahn, D.,Heinz, D.W.
High resolution crystal structure of a Mg2+-dependent porphobilinogen synthase.
J.Mol.Biol., 289:591-602, 1999

PubMed Abstract: Common to the biosynthesis of all known tetrapyrroles is the condensation of two molecules of 5-aminolevulinic acid to the pyrrole porphobilinogen catalyzed by the enzyme porphobilinogen synthase (PBGS). Two major classes of PBGS are known. Zn2+-dependent PBGSs are found in mammals, yeast and some bacteria including Escherichia coli, while Mg2+-dependent PBGSs are present mainly in plants and other bacteria. The crystal structure of the Mg2+-dependent PBGS from the human pathogen Pseudomonas aeruginosa in complex with the competitive inhibitor levulinic acid (LA) solved at 1.67 A resolution shows a homooctameric enzyme that consists of four asymmetric dimers. The monomers in each dimer differ from each other by having a "closed" and an "open" active site pocket. In the closed subunit, the active site is completely shielded from solvent by a well-defined lid that is partially disordered in the open subunit. A single molecule of LA binds to a mainly hydrophobic pocket in each monomer where it is covalently attached via a Schiff base to an active site lysine residue. Whereas no metal ions are found in the active site of both monomers, a single well-defined and highly hydrated Mg2+is present only in the closed form about 14 A away from the Schiff base forming nitrogen atom of the active site lysine. We conclude that the observed differences in the active sites of both monomers might be induced by Mg2+-binding to this remote site and propose a structure-based mechanism for this allosteric Mg2+in rate enhancement.

PubMed: 10356331
DOI: 10.1006/jmbi.1999.2808

Experimental method

X-RAY DIFFRACTION (1.67 Å)