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PMID: 16225687 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Natural history of S-adenosylmethionine-binding proteins.

BMC structural biology ·Vol. 5 ·2005-10-14 ·Pages 19

Kozbial PZ, Mushegian AR

Abstract

S-adenosylmethionine is a source of diverse chemical groups used in biosynthesis and modification of virtually every class of biomolecules. The most notable reaction requiring S-adenosylmethionine, transfer of methyl group, is performed by a large class of enzymes, S-adenosylmethionine-dependent methyltransferases, which have been the focus of considerable structure-function studies. Evolutionary trajectories of these enzymes, and especially of other classes of S-adenosylmethionine-binding proteins, nevertheless, remain poorly understood. We addressed this issue by computational comparison of sequences and structures of various S-adenosylmethionine-binding proteins. Two widespread folds, Rossmann fold and TIM barrel, have been repeatedly used in evolution for diverse types of S-adenosylmethionine conversion. There were also cases of recruitment of other relatively common folds for S-adenosylmethionine binding. Several classes of proteins have unique unrelated folds, specialized for just one type of chemistry and unified by the theme of internal domain duplications. In several cases, functional divergence is evident, when evolutionarily related enzymes have changed the mode of binding and the type of chemical transformation of S-adenosylmethionine. There are also instances of functional convergence, when biochemically similar processes are performed by drastically different classes of S-adenosylmethionine-binding proteins. Comparison of remote sequence similarities and analysis of phyletic patterns suggests that the last universal common ancestor of cellular life had between 10 and 20 S-adenosylmethionine-binding proteins from at least 5 fold classes, providing for S-adenosylmethionine formation, polyamine biosynthesis, and methylation of several substrates, including nucleic acids and peptide chain release factor. We have observed several novel relationships between families that were not known to be related before, and defined 15 large superfamilies of SAM-binding proteins, at least 5 of which may have been represented in the last common ancestor.

MeSH Terms
Amino Acid Sequence Animals Binding Sites Biochemistry/methods Carboxy-Lyases/chemistry Carrier Proteins/chemistry Catalytic Domain Computational Biology/methods Humans Models, Molecular Molecular Sequence Data Peptides/chemistry Phylogeny Porphyrins/chemistry Protein Binding Protein Conformation Protein Folding Protein Structure, Tertiary Proteins/chemistry,classification Proteomics/methods S-Adenosylmethionine/chemistry Sequence Homology, Amino Acid
Chemicals
Carrier Proteins Peptides Porphyrins Proteins S-Adenosylmethionine Carboxy-Lyases
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Kozbial Piotr Z
Stowers Institute for Medical Research, Kansas City, MO 64110, USA. pzk@stowers-institute.org
Mushegian Arcady R
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Article Info
Journal
BMC structural biology
Abbr.
BMC Struct Biol
ISSN
1472-6807
DOI
10.1186/1472-6807-5-19
Email
pzk@stowers-institute.org
Published
2005-10-14
Epub
2005-00-14
Pages
19
Language
English
Region
England
NLM ID
101088689
PMCID
PMC1282579
Subset
IM
External Links
PubMed source DOI: 10.1186/1472-6807-5-19 PMC Full Text View journal details
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