Selenocysteine - Revision history

Eric Martz: /* Visualization */

Eric Martz — Fri, 21 Jan 2022 01:27:51 GMT

Visualization

←Older revision		Revision as of 01:27, 21 January 2022
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	[http://firstglance.jmol.org/fg.htm?mol=6hkq View 6HKQ in FirstGlance in Jmol].		[http://firstglance.jmol.org/fg.htm?mol=6hkq View 6HKQ in FirstGlance in Jmol].
	:1. Look for the "Focus Box" (in the upper left panel, scroll down to the bottom ), and there click on "Find..".		:1. Look for the "Focus Box" (in the upper left panel, scroll down to the bottom ), and there click on "Find..".
-	:2. Enter "sec" into the Find slot.	+	:2. Enter '''sec''' into the Find slot.

	To examine in detail what contacts the Sec46 (continuing from step 2 above):		To examine in detail what contacts the Sec46 (continuing from step 2 above):

Eric Martz: /* Visualization */

Eric Martz — Fri, 21 Jan 2022 01:27:31 GMT

Visualization

←Older revision		Revision as of 01:27, 21 January 2022
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	==Visualization==		==Visualization==
	[http://firstglance.jmol.org/fg.htm?mol=6hkq View 6HKQ in FirstGlance in Jmol].		[http://firstglance.jmol.org/fg.htm?mol=6hkq View 6HKQ in FirstGlance in Jmol].
-	:1. Look for the "Focus Box", and there click on "Find..".	+	:1. Look for the "Focus Box" (in the upper left panel, scroll down to the bottom ), and there click on "Find..".
	:2. Enter "sec" into the Find slot.		:2. Enter "sec" into the Find slot.

Eric Martz: /* Occurrence */

Eric Martz — Fri, 21 Jan 2022 01:26:34 GMT

Occurrence

←Older revision		Revision as of 01:26, 21 January 2022
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	In January, 2022, '''76 entries''' in the [[wwPDB]] contain Sec. An example of naturally-occuring Sec is human glutathione peroxidase 4, where Sec46 occurs in the catalytic site. [[6hn3]] is the wild type, while [[6hkq]] has an inhibitor covalently bound to the Sec.		In January, 2022, '''76 entries''' in the [[wwPDB]] contain Sec. An example of naturally-occuring Sec is human glutathione peroxidase 4, where Sec46 occurs in the catalytic site. [[6hn3]] is the wild type, while [[6hkq]] has an inhibitor covalently bound to the Sec.
		+
		+	==Visualization==
		+	[http://firstglance.jmol.org/fg.htm?mol=6hkq View 6HKQ in FirstGlance in Jmol].
		+	:1. Look for the "Focus Box", and there click on "Find..".
		+	:2. Enter "sec" into the Find slot.
		+
		+	To examine in detail what contacts the Sec46 (continuing from step 2 above):
		+	:3. Click on "Contacts & Non-Covalent Interactions" in the Tools tab.
		+	:4. Check "Atoms with Halos" as the target.
		+	:5. Click "Show atoms contacting target".
		+	Explore using the tools that are now available in the lower left "Contacts Shown" panel.

	==Translation from UGA Stop Codon==		==Translation from UGA Stop Codon==

Eric Martz: /* Occurrence */

Eric Martz — Fri, 21 Jan 2022 01:20:13 GMT

Occurrence

←Older revision		Revision as of 01:20, 21 January 2022
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	Sec occurs in all domains of life, including bacteria, archaea, and eukaryota<ref>PMID: 19477234</ref><ref name'wp'>[http://en.wikipedia.org/wiki/Selenocysteine Selenocysteine in Wikipedia]</ref>. Sec occurs in the active sites of enzymes involved in removing reactive oxygen species, and in thyroid hormone activation<ref name='Palioura' />. For more examples, please see [http://en.wikipedia.org/wiki/Selenocysteine Selenocysteine in Wikipedia].		Sec occurs in all domains of life, including bacteria, archaea, and eukaryota<ref>PMID: 19477234</ref><ref name'wp'>[http://en.wikipedia.org/wiki/Selenocysteine Selenocysteine in Wikipedia]</ref>. Sec occurs in the active sites of enzymes involved in removing reactive oxygen species, and in thyroid hormone activation<ref name='Palioura' />. For more examples, please see [http://en.wikipedia.org/wiki/Selenocysteine Selenocysteine in Wikipedia].

-	~~[http://xray.bmc.uu.se/hicup/ HIC-Up] reports the occurrence of Sec in [http://xray.bmc.uu.se/hicup/CSE/ 11~~ entries] in the [[~~PDB~~]]. ~~The highest~~ [[~~Resolution\|resolution~~]] ~~entry~~ is [[~~1kqf~~]] ~~(1.6 Å), with~~ Sec ~~at 196 in chain A. To see it, go to [[1kqf]] and click on CSE under Non-Standard Residues~~.	+	In January, 2022, '''76 entries''' in the [[wwPDB]] contain Sec. An example of naturally-occuring Sec is human glutathione peroxidase 4, where Sec46 occurs in the catalytic site. [[6hn3]] is the wild type, while [[6hkq]] has an inhibitor covalently bound to the Sec.

	==Translation from UGA Stop Codon==		==Translation from UGA Stop Codon==

Eric Martz at 01:01, 21 January 2022

Eric Martz — Fri, 21 Jan 2022 01:01:31 GMT

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-	), is called the 21st [[Amino Acids\|amino acid]]<ref name='21st'>PMID: 11028985</ref>. It is incorporated into rare proteins in all domains of life, and is essential for life. When the UGA stop codon is accompanied by a [[#Translation from UGA Stop Codon\|suitable signal]], it is translated as Sec instead of stopping translation. In the [[PDB]], the code for [[hetero]] group Sec is '''~~CSE~~'''. For more information beyond what is below, please see [http://en.wikipedia.org/wiki/Selenocysteine Selenocysteine in Wikipedia].	+	), is called the 21st [[Amino Acids\|amino acid]]<ref name='21st'>PMID: 11028985</ref>. It is incorporated into rare proteins in all domains of life, and is essential for life. When the UGA stop codon is accompanied by a [[#Translation from UGA Stop Codon\|suitable signal]], it is translated as Sec instead of stopping translation. In the [[PDB]], the code for [[Hetero atoms\|hetero]] group Sec is '''SEC'''<ref>Prior to remediations of the [[wwPDB]] done after 2010, some Sec in the wwPDB was coded CSE.</ref>. For more information beyond what is below, please see [http://en.wikipedia.org/wiki/Selenocysteine Selenocysteine in Wikipedia].

	==Importance==		==Importance==

Eric Martz: /* Translation from UGA Stop Codon */

Eric Martz — Tue, 14 Aug 2018 20:20:53 GMT

Translation from UGA Stop Codon

←Older revision		Revision as of 20:20, 14 August 2018
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	==Translation from UGA Stop Codon==		==Translation from UGA Stop Codon==

-	During translation of mRNA, UGA is normally interpreted as a stop codon. However, when a special Sec-insertion sequence (SECIS), a stem-loop structure, is present downstream (in the untranslated region in mammals), UGA is translated as Sec<ref name='21st' /><ref name='Palioura' />. This involves the interaction of this stem-loop structure with specialized elongation factors called SelB in bacteria and EFSec in humans<ref name='Palioura' />.	+	During translation of mRNA, UGA is normally interpreted as a stop codon. However, when a special Sec-insertion sequence (SECIS), a stem-loop structure, is present downstream (in the untranslated region in mammals), UGA is translated as Sec<ref name='21st' /><ref name='Palioura' />. This involves the interaction of this stem-loop structure with specialized elongation factors called [[SelB]] in bacteria and EFSec in humans<ref name='Palioura' />.

	==Structure and Synthesis==		==Structure and Synthesis==

Eric Martz: /* Notes and References */

Eric Martz — Tue, 14 Aug 2018 20:20:05 GMT

Notes and References

←Older revision		Revision as of 20:20, 14 August 2018
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	The [[X-ray crystallography\|crystal]] structure of the complex that converts Ser-tRNA<sup>Sec</sup> to Sec-tRNA<sup>Sec</sup> ('''[[3hl2]]''') was reported in 2009<ref name='Palioura'>PMID: 19608919</ref>. This consists of ''O''-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS) complexed to tRNA<sup>Sec</sup>, phosphoserine, and thiophosphate. The authors conclude that this structure, together with enzymology, supports a pyridoxal phosphate-dependent mechanism.		The [[X-ray crystallography\|crystal]] structure of the complex that converts Ser-tRNA<sup>Sec</sup> to Sec-tRNA<sup>Sec</sup> ('''[[3hl2]]''') was reported in 2009<ref name='Palioura'>PMID: 19608919</ref>. This consists of ''O''-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS) complexed to tRNA<sup>Sec</sup>, phosphoserine, and thiophosphate. The authors conclude that this structure, together with enzymology, supports a pyridoxal phosphate-dependent mechanism.
		+
		+	==See Also==
		+	*[[Selenomethionine]]
		+	*[[Selenocysteine synthase]]
		+	*Selenocysteine-specific elongation factor [[SelB]]

	==Notes and References==		==Notes and References==
	<references />		<references />

Eric Martz: /* Occurrence */ adding content

Eric Martz — Tue, 28 Jul 2009 21:52:07 GMT

Occurrence - adding content

←Older revision		Revision as of 21:52, 28 July 2009
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	==Occurrence==		==Occurrence==

-	Sec occurs in all domains of life, including bacteria, archaea, and eukaryota<ref name'wp'>[http://en.wikipedia.org/wiki/Selenocysteine Selenocysteine in Wikipedia]</ref>. Sec occurs in the active sites of enzymes involved in removing reactive oxygen species, and in thyroid hormone activation<ref name='Palioura' />. For more examples, please see [http://en.wikipedia.org/wiki/Selenocysteine Selenocysteine in Wikipedia].	+	Sec occurs in all domains of life, including bacteria, archaea, and eukaryota<ref>PMID: 19477234</ref><ref name'wp'>[http://en.wikipedia.org/wiki/Selenocysteine Selenocysteine in Wikipedia]</ref>. Sec occurs in the active sites of enzymes involved in removing reactive oxygen species, and in thyroid hormone activation<ref name='Palioura' />. For more examples, please see [http://en.wikipedia.org/wiki/Selenocysteine Selenocysteine in Wikipedia].

	[http://xray.bmc.uu.se/hicup/ HIC-Up] reports the occurrence of Sec in [http://xray.bmc.uu.se/hicup/CSE/ 11 entries] in the [[PDB]]. The highest [[Resolution\|resolution]] entry is [[1kqf]] (1.6 Å), with Sec at 196 in chain A. To see it, go to [[1kqf]] and click on CSE under Non-Standard Residues.		[http://xray.bmc.uu.se/hicup/ HIC-Up] reports the occurrence of Sec in [http://xray.bmc.uu.se/hicup/CSE/ 11 entries] in the [[PDB]]. The highest [[Resolution\|resolution]] entry is [[1kqf]] (1.6 Å), with Sec at 196 in chain A. To see it, go to [[1kqf]] and click on CSE under Non-Standard Residues.

Eric Martz: /* Structure and Synthesis */ polishing

Eric Martz — Tue, 28 Jul 2009 21:44:22 GMT

Structure and Synthesis - polishing

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	Sec differs from the [[Amino Acids\|20 standard amino acids]] because, in all domains of life, it lacks its own tRNA synthetase, and is synthesized from Ser covalently linked to tRNA<sup>Sec</sup>.		Sec differs from the [[Amino Acids\|20 standard amino acids]] because, in all domains of life, it lacks its own tRNA synthetase, and is synthesized from Ser covalently linked to tRNA<sup>Sec</sup>.

-	The [[X-ray crystallography\|crystal]] structure of the complex that converts Ser-tRNA<sup>Sec</sup> to Sec-tRNA<sup>Sec</sup> ('''[[3hl2]]''') was reported in 2009<ref name='Palioura'>PMID: 19608919</ref>. This consists of ''O''-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS) complexed to tRNA<sup>Sec</sup>, phosphoserine, and thiophosphate. The authors conclude that this structure, together with ~~enzyme assays~~, supports a pyridoxal phosphate-dependent mechanism.	+	The [[X-ray crystallography\|crystal]] structure of the complex that converts Ser-tRNA<sup>Sec</sup> to Sec-tRNA<sup>Sec</sup> ('''[[3hl2]]''') was reported in 2009<ref name='Palioura'>PMID: 19608919</ref>. This consists of ''O''-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS) complexed to tRNA<sup>Sec</sup>, phosphoserine, and thiophosphate. The authors conclude that this structure, together with enzymology, supports a pyridoxal phosphate-dependent mechanism.

	==Notes and References==		==Notes and References==
	<references />		<references />

Eric Martz: adding content

Eric Martz — Tue, 28 Jul 2009 21:42:16 GMT

adding content

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