Journal ArticleDOI
A new UAG-encoded residue in the structure of a methanogen methyltransferase.
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The UAG-encoded residue in a 1.55 angstrom resolution structure of the Methanosarcina barkerimonomethylamine methyltransferase (MtmB) reveals a homohexamer comprised of individual subunits with a TIM barrel fold that appears consistent with a lysine in amide-linkage to (4R,5R)-4-substituted-pyrroline-5-carboxylate.Abstract:
Genes encoding methanogenic methylamine methyltransferases all contain an in-frame amber (UAG) codon that is read through during translation. We have identified the UAG-encoded residue in a 1.55 angstrom resolution structure of the Methanosarcina barkeri monomethylamine methyltransferase (MtmB). This structure reveals a homohexamer comprised of individual subunits with a TIM barrel fold. The electron density for the UAG-encoded residue is distinct from any of the 21 natural amino acids. Instead it appears consistent with a lysine in amide-linkage to (4R,5R)-4-substituted-pyrroline-5-carboxylate. We suggest that this amino acid be named l-pyrrolysine.read more
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Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea.
Yuchen Liu,William B. Whitman +1 more
TL;DR: The ecology of methanogens highlights their complex interactions with other anaerobes and the physical and chemical factors controlling their function.
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Acetogenesis and the Wood-Ljungdahl Pathway of CO2 Fixation
TL;DR: The Wood-Ljungdahl pathway of CO(2) fixation involves this type of stepwise process and has intrigued chemists, biochemists, and microbiologists for many decades.
Journal ArticleDOI
On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells
TL;DR: The universal ancestor the authors infer was not a free-living cell, but rather was confined to the naturally chemiosmotic, FeS compartments within which the synthesis of its constituents occurred, leading to the emergence of prokaryotic lineages from inorganic confines.
Journal ArticleDOI
The many faces of vitamin B12: catalysis by cobalamin-dependent enzymes.
TL;DR: Understanding of the reaction mechanisms of B12 enzymes has been greatly enhanced by the availability of large amounts of enzyme that have afforded detailed structure-function studies, and these recent advances are the subject of this review.
Journal ArticleDOI
Radical S-Adenosylmethionine Enzymes
TL;DR: This Review will begin by summarizing unifying features of radical SAM enzymes, and in subsequent sections delve further into the biochemical, spectroscopic, structural, and mechanistic details for those enzymes that catalyze an amazingly diverse set of reactions.
References
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Journal ArticleDOI
PROCHECK: a program to check the stereochemical quality of protein structures
TL;DR: The PROCHECK suite of programs as mentioned in this paper provides a detailed check on the stereochemistry of a protein structure and provides an assessment of the overall quality of the structure as compared with well refined structures of the same resolution.
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MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
TL;DR: The MOLSCRIPT program as discussed by the authors produces plots of protein structures using several different kinds of representations, including simple wire models, ball-and-stick models, CPK models and text labels.
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CATH – a hierarchic classification of protein domain structures
Christine A. Orengo,A.D. Michie,Susan Jones,David T. Jones,Mark B. Swindells,Janet M. Thornton +5 more
TL;DR: Analysis of the structural families generated by CATH reveals the prominent features of protein structure space and a database of well-characterised protein structure families will facilitate the assignment of structure-function/evolution relationships to both known and newly determined protein structures.
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XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density.
TL;DR: XFit as mentioned in this paper is a model-building and map viewing program in XView that is used by the structural biology community including researchers in the fields of crystallography, molecular modeling, and electron microscopy.
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Biochemistry of methanogenesis: a tribute to Marjory Stephenson:1998 Marjory Stephenson Prize Lecture
TL;DR: In 1933, Stephenson & Stickland published that they had isolated from river mud, by the single cell technique, a methanogenic organism capable of growth in an inorganic medium with formate as the sole carbon source.