3EP6

Human AdoMetDC D174N mutant complexed with S-Adenosylmethionine methyl ester and no putrescine bound

Summary for 3EP6

• Entry DOI: 10.2210/pdb3ep6/pdb
• Related: 1I72 1I79 1I7B 1I7C 1I7M 1JEN 3EP3 3EP4 3EP5 3EP7 3EP8 3EP9 3EPA 3EPB
• Descriptor: S-adenosylmethionine decarboxylase beta chain, S-adenosylmethionine decarboxylase alpha chain, PYRUVIC ACID, ... (5 entities in total)
• Functional Keywords: adometdc with mutation in putrescine binding site, decarboxylase, lyase, pyruvate, s-adenosyl-l-methionine, spermidine biosynthesis, zymogen
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 38084.35

Authors

Bale, S.,Lopez, M.M.,Makhatadze, G.I.,Fang, Q.,Pegg, A.E.,Ealick, S.E. (deposition date: 2008-09-29, release date: 2008-12-23, Last modification date: 2023-11-15)

Primary citation

Bale, S.,Lopez, M.M.,Makhatadze, G.I.,Fang, Q.,Pegg, A.E.,Ealick, S.E.
Structural Basis for Putrescine Activation of Human S-Adenosylmethionine Decarboxylase.
Biochemistry, 47:13404-13417, 2008

PubMed Abstract: Putrescine (1,4-diaminobutane) activates the autoprocessing and decarboxylation reactions of human S-adenosylmethionine decarboxylase (AdoMetDC), a critical enzyme in the polyamine biosynthetic pathway. In human AdoMetDC, putrescine binds in a buried pocket containing acidic residues Asp174, Glu178, and Glu256. The pocket is away from the active site but near the dimer interface; however, a series of hydrophilic residues connect the putrescine binding site and the active site. Mutation of these acidic residues modulates the effects of putrescine. D174N, E178Q, and E256Q mutants were expressed and dialyzed to remove putrescine and studied biochemically using X-ray crystallography, UV-CD spectroscopy, analytical ultracentrifugation, and ITC binding studies. The results show that the binding of putrescine to the wild type dimeric protein is cooperative. The D174N mutant does not bind putrescine, and the E178Q and E256Q mutants bind putrescine weakly with no cooperativity. The crystal structure of the mutants with and without putrescine and their complexes with S-adenosylmethionine methyl ester were obtained. Binding of putrescine results in a reorganization of four aromatic residues (Phe285, Phe315, Tyr318, and Phe320) and a conformational change in the loop 312-320. The loop shields putrescine from the external solvent, enhancing its electrostatic and hydrogen bonding effects. The E256Q mutant with putrescine added shows an alternate conformation of His243, Glu11, Lys80, and Ser229, the residues that link the active site and the putrescine binding site, suggesting that putrescine activates the enzyme through electrostatic effects and acts as a switch to correctly orient key catalytic residues.

PubMed: 19053272
DOI: 10.1021/bi801732m

Experimental method

X-RAY DIFFRACTION (1.7 Å)