PDBsum entry 3epb

Lyase

PDB id: 3epb

Contents

Protein chains

55 a.a. *

253 a.a. *

Ligands

PUT

PYR

Waters ×194

* Residue conservation analysis

PDB id:

3epb

Name:

Lyase

Title:

Human adometdc e256q mutant complexed with putrescine

Structure:

S-adenosylmethionine decarboxylase beta chain. Chain: b. Fragment: unp residues 1-67. Synonym: adometdc, samdc. Engineered: yes. S-adenosylmethionine decarboxylase alpha chain. Chain: a. Fragment: unp residues 69-328. Synonym: adometdc, samdc.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: amd1, amd. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.75Å R-factor: 0.238 R-free: 0.253

Authors:

S.Bale,M.M.Lopez,G.I.Makhatadze,Q.Fang,A.E.Pegg,S.E.Ealick

Key ref:

S.Bale et al. (2008). Structural basis for putrescine activation of human S-adenosylmethionine decarboxylase. Biochemistry, 47, 13404-13417. PubMed id: 19053272

Date:

29-Sep-08 Release date: 23-Dec-08

Protein chain

P17707  (DCAM_HUMAN) -  S-adenosylmethionine decarboxylase proenzyme from Homo sapiens

Seq: 334 a.a.

Struc: 55 a.a.

Protein chain

P17707  (DCAM_HUMAN) -  S-adenosylmethionine decarboxylase proenzyme from Homo sapiens

Seq: 334 a.a.

Struc: 253 a.a.*

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

Enzyme reactions

• Enzyme class: Chains B, A: E.C.4.1.1.50 - adenosylmethionine decarboxylase.
• Pathway: Spermine Biosynthesis
• Reaction: S-adenosyl-L-methionine + H⁺ = S-adenosyl 3-(methylsulfanyl)propylamine + CO2
• Cofactor: Pyruvate

Pyruvate (Bound ligand (Het Group name = PYR) matches with 83.33% similarity)

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

reference

Biochemistry 47:13404-13417 (2008)

PubMed id: 19053272

Structural basis for putrescine activation of human S-adenosylmethionine decarboxylase.

S.Bale, M.M.Lopez, G.I.Makhatadze, Q.Fang, A.E.Pegg, S.E.Ealick.

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.