6ZNB

PHAGE SAM LYASE IN APO STATE

This is a non-PDB format compatible entry.

Summary for 6ZNB

• Entry DOI: 10.2210/pdb6znb/pdb
• Related: 6ZM9 6ZMG
• Descriptor: Phage SAM lyase Svi3-3, PHOSPHATE ION (3 entities in total)
• Functional Keywords: sam lyase, s-adenosyl methionine, phage, lyase
• Biological source: Bacteriophage sp.
• Total number of polymer chains: 1
• Total formula weight: 16493.41

Authors

Eckhard, U.,Kanchugal P, S.,Selmer, M. (deposition date: 2020-07-06, release date: 2021-02-24, Last modification date: 2024-01-31)

Primary citation

Guo, X.,Soderholm, A.,Kanchugal P, S.,Isaksen, G.V.,Warsi, O.,Eckhard, U.,Triguis, S.,Gogoll, A.,Jerlstrom-Hultqvist, J.,Aqvist, J.,Andersson, D.I.,Selmer, M.
Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family.
Elife, 10:-, 2021

PubMed Abstract: The first S-adenosyl methionine (SAM) degrading enzyme (SAMase) was discovered in bacteriophage T3, as a counter-defense against the bacterial restriction-modification system, and annotated as a SAM hydrolase forming 5'-methyl-thioadenosine (MTA) and L-homoserine. From environmental phages, we recently discovered three SAMases with barely detectable sequence similarity to T3 SAMase and without homology to proteins of known structure. Here, we present the very first phage SAMase structures, in complex with a substrate analogue and the product MTA. The structure shows a trimer of alpha-beta sandwiches similar to the GlnB-like superfamily, with active sites formed at the trimer interfaces. Quantum-mechanical calculations, thin-layer chromatography, and nuclear magnetic resonance spectroscopy demonstrate that this family of enzymes are not hydrolases but lyases forming MTA and L-homoserine lactone in a unimolecular reaction mechanism. Sequence analysis and in vitro and in vivo mutagenesis support that T3 SAMase belongs to the same structural family and utilizes the same reaction mechanism.

PubMed: 33567250
DOI: 10.7554/eLife.61818

Experimental method

X-RAY DIFFRACTION (2.8 Å)