SAM riboswitch (S box leader)

The SAM riboswitch (also known as the S-box leader and now also called the SAM-I riboswitch) is found upstream of a number of genes which code for proteins involved in methionine or cysteine biosynthesis in Gram-positive bacteria. Two SAM riboswitches in "Bacillus subtilis" that were experimentally studied act at the level of transcription termination control. The predicted secondary structure consists of a complex stem-loop region followed by a single stem loop terminator region. An alternative and mutually exclusive form involves bases in the 3' segment of helix 1 with those in the 5' region of helix 5 to form a structure termed the anti-terminator form.cite journal | author = Grundy FJ, Henkin TM | title = The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria | journal = Mol. Microbiol. | volume = 30 | issue = 4 | pages = 737–49 | year = 1998 | pmid = 10094622 | doi = | issn = ] [cite journal | last = Epshtein | first = V | coauthors = Mironov AS, Nudler E | year = 2003 | title = The riboswitch-mediated control of sulfur metabolism in bacteria | journal = Proc Natl Acad Sci U S A | volume = 100 | pages = 5052–5056 | pmid = 12702767 | doi = 10.1073/pnas.0531307100] [cite journal | author = Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR | title = An mRNA structure that controls gene expression by binding S-adenosylmethionine | journal = Nat. Struct. Biol. | volume = 10 | issue = 9 | pages = 701–7 | year = 2003 | pmid = 12910260 | doi = 10.1038/nsb967 | issn = ] However, many SAM riboswitches are likely to regulate gene expression at the level of translation.

tructure organization

The structure of the SAM riboswitch has been determined with X-ray crystallography. [cite journal | last = Montange | first = RK | coauthors = Batey RT | year = 2006 | title = Structure of the S-adenosylmethionine riboswitch regulatory mRNA element | journal = Nature. | volume = 441 | pages = 1172–1175 | pmid = 16810258 | doi = 10.1038/nature04819] The SAM riboswitch is organized around a four way junction, with two sets of coaxially stacked helices arranged side-by-side. These stacks are held together by a pseudoknot formed between the loop on the end of stem P2 and the J3/4 joining region. The formation of the pseudoknot is facillitated by a protein-independent kink-turn which induced a 100 ^o bend into P2. Both the kink-turn and the pseudoknot are critical to the establishment of the global fold and productive binding. The binding pocket is split between conserved, tandem AU pairs in stem P1 and the conserved asymmetric bulge in stem P3. The adenosyl and methionine main-chain moieties of S-Adenosyl methionine (SAM) are recognized through hydrogen-bonding into the bulge in P3. The methyl group is recognized indirectly through the charged sulfur, which forms an electrostatic interaction with the negative surface potential in the minor groove of P1. This negative surface is created by the tandem AU pairs.

Two classes of SAM-binding riboswitches are known that have entirely different structures to SAM-I riboswitches, these are SAM-II riboswitches and SAM-III riboswitches. A fourth type, SAM-IV riboswitches, appears to share a similar ligand-binding site with that of SAM-I riboswitches, but in the context of a distinct scaffold.

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