1MT1

The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannaschii

Summary for 1MT1

• Entry DOI: 10.2210/pdb1mt1/pdb
• Descriptor: PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN, PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN, AGMATINE, ... (4 entities in total)
• Functional Keywords: pyruvoyl group, pyruvate, agmatine, arginine, lyase
• Biological source: Methanocaldococcus jannaschii; More
• Total number of polymer chains: 12
• Total formula weight: 108692.37

Authors

Tolbert, W.D.,Graham, D.E.,White, R.H.,Ealick, S.E. (deposition date: 2002-09-20, release date: 2003-03-25, Last modification date: 2024-10-30)

Primary citation

Tolbert, W.D.,Graham, D.E.,White, R.H.,Ealick, S.E.
Pyruvoyl-Dependent Arginine Decarboxylase from Methanococcus jannaschii: Crystal Structures of the Self-Cleaved and S53A Proenzyme Forms
Structure, 11:285-294, 2003

PubMed Abstract: The three-dimensional structure of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii was determined at 1.4 A resolution. The pyruvoyl group of arginine decarboxylase is generated by an autocatalytic internal serinolysis reaction at Ser53 in the proenzyme resulting in two polypeptide chains. The structure of the nonprocessing S53A mutant was also determined. The active site of the processed enzyme unexpectedly contained the reaction product agmatine. The crystal structure confirms that arginine decarboxylase is a homotrimer. The protomer fold is a four-layer alphabetabetaalpha sandwich with topology similar to pyruvoyl-dependent histidine decarboxylase. Highly conserved residues Asn47, Ser52, Ser53, Ile54, and Glu109 are proposed to play roles in the self-processing reaction. Agmatine binding residues include the C terminus of the beta chain (Ser52) from one protomer and the Asp35 side chain and the Gly44 and Val46 carbonyl oxygen atoms from an adjacent protomer. Glu109 is proposed to play a catalytic role in the decarboxylation reaction.

PubMed: 12623016
DOI: 10.1016/S0969-2126(03)00026-1

Experimental method

X-RAY DIFFRACTION (2.2 Å)