User:Christian Fjeld/Sandbox 1 - Revision history

Christian Fjeld at 14:12, 3 May 2018

Christian Fjeld — Thu, 03 May 2018 14:12:43 GMT

←Older revision		Revision as of 14:12, 3 May 2018
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	Mutations in LARS2, the mitochondrial version of the enzyme, have been linked to Perrault syndrome characterized by premature ovarian failure in females and progressive hearing loss in both sexes<ref>doi: 10.1016/j.jmb.2009.04.073</ref>		Mutations in LARS2, the mitochondrial version of the enzyme, have been linked to Perrault syndrome characterized by premature ovarian failure in females and progressive hearing loss in both sexes<ref>doi: 10.1016/j.jmb.2009.04.073</ref>

-	----

	== Structure ==		== Structure ==

	LARS is composed of five domains, two catalyticly active domains; the catalytic and editing domains, one tRNA recognition domain; the anticodon binding domain, and two domains that pivot over the aminoacylation site; the leucine-specific and zinc binding domains. Together, these five domains carry out the task of aminoacylating uncharged tRNA and hydrolysing mischarged tRNA with a high specificity for tRNA<sup>leu</sup>.		LARS is composed of five domains, two catalyticly active domains; the catalytic and editing domains, one tRNA recognition domain; the anticodon binding domain, and two domains that pivot over the aminoacylation site; the leucine-specific and zinc binding domains. Together, these five domains carry out the task of aminoacylating uncharged tRNA and hydrolysing mischarged tRNA with a high specificity for tRNA<sup>leu</sup>.
		+

	=== Catalytic Domain ===		=== Catalytic Domain ===
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	== 3D Structure of LARS ==		== 3D Structure of LARS ==
-

	{{#tree:id=OrganizedByTopic\|openlevels=0\|		{{#tree:id=OrganizedByTopic\|openlevels=0\|
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	**[[4k48]]<br />		**[[4k48]]<br />
	}}		}}
		+
		+
	== References ==		== References ==
	<references/>		<references/>

Christian Fjeld at 14:11, 3 May 2018

Christian Fjeld — Thu, 03 May 2018 14:11:17 GMT

←Older revision		Revision as of 14:11, 3 May 2018
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	Mutations in LARS2, the mitochondrial version of the enzyme, have been linked to Perrault syndrome characterized by premature ovarian failure in females and progressive hearing loss in both sexes<ref>doi: 10.1016/j.jmb.2009.04.073</ref>		Mutations in LARS2, the mitochondrial version of the enzyme, have been linked to Perrault syndrome characterized by premature ovarian failure in females and progressive hearing loss in both sexes<ref>doi: 10.1016/j.jmb.2009.04.073</ref>
		+
		+	----

	== Structure ==		== Structure ==
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	{{Template:ColorKey_ConSurf}}		{{Template:ColorKey_ConSurf}}

		+	Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
	</StructureSection>		</StructureSection>

	== 3D Structure of LARS ==		== 3D Structure of LARS ==

-	~~Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}~~	+
	{{#tree:id=OrganizedByTopic\|openlevels=0\|		{{#tree:id=OrganizedByTopic\|openlevels=0\|

Christian Fjeld at 14:09, 3 May 2018

Christian Fjeld — Thu, 03 May 2018 14:09:47 GMT

←Older revision		Revision as of 14:09, 3 May 2018
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	=== Editing Domain ===		=== Editing Domain ===

-	The <scene name='78/786656/Editing/1'>editing domain</scene> of LARS is responsible for hydrolysing mischarged tRNA, such as ile-tRNA<sup>leu</sup>, and releasing it for a subsequent round of aminoacylation. This <scene name='78/786656/Editing_conformation/1'>editing function</scene> allows cells to achieve a tRNA charging error rate of less than 1:10,000<ref>doi: 10.1016/j.jmb.2009.04.073</ref>. The domain itself is an β sandwich connected to the catalytic domain by a flexible loop that allows ~~a hinge action to bind~~ aminoacylated tRNAs for error checking.	+	The <scene name='78/786656/Editing/1'>editing domain</scene> of LARS is responsible for hydrolysing mischarged tRNA, such as ile-tRNA<sup>leu</sup>, and releasing it for a subsequent round of aminoacylation. This <scene name='78/786656/Editing_conformation/1'>editing function</scene> allows cells to achieve a tRNA charging error rate of less than 1:10,000<ref>doi: 10.1016/j.jmb.2009.04.073</ref>. The domain itself is an β sandwich connected to the catalytic domain by a flexible loop that allows binding of aminoacylated tRNAs for error checking.

	[[Image:Editing2.JPG]]		[[Image:Editing2.JPG]]

Christian Fjeld at 14:08, 3 May 2018

Christian Fjeld — Thu, 03 May 2018 14:08:25 GMT

←Older revision		Revision as of 14:08, 3 May 2018
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	=== Editing Domain ===		=== Editing Domain ===

-	The <scene name='78/786656/Editing/1'>editing domain</scene> of LARS is responsible for hydrolysing mischarged tRNA, such as ile-tRNA<sup>leu</sup>, and releasing it for a subsequent round of aminoacylation. This editing function allows cells to achieve a tRNA charging error rate of less than 1:10,000<ref>doi: 10.1016/j.jmb.2009.04.073</ref>. The domain itself is an β sandwich connected to the catalytic domain by a flexible loop that allows a hinge action to bind aminoacylated tRNAs for error checking.	+	The <scene name='78/786656/Editing/1'>editing domain</scene> of LARS is responsible for hydrolysing mischarged tRNA, such as ile-tRNA<sup>leu</sup>, and releasing it for a subsequent round of aminoacylation. This <scene name='78/786656/Editing_conformation/1'>editing function</scene> allows cells to achieve a tRNA charging error rate of less than 1:10,000<ref>doi: 10.1016/j.jmb.2009.04.073</ref>. The domain itself is an β sandwich connected to the catalytic domain by a flexible loop that allows a hinge action to bind aminoacylated tRNAs for error checking.

	[[Image:Editing2.JPG]]		[[Image:Editing2.JPG]]

Christian Fjeld at 14:03, 3 May 2018

Christian Fjeld — Thu, 03 May 2018 14:03:27 GMT

←Older revision		Revision as of 14:03, 3 May 2018
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	=== Catalytic Domain ===		=== Catalytic Domain ===
-	[[Image:CatalyticSite.png \| thumb]]	+	[[Image:CatalyticSite.png \| thumb \| Active site with leucyl adenylate analog and A76]]
	The <scene name='78/786656/Catalytic/1'>catalytic domain</scene> is responsible for the two step process of charging leucine on to tRNA<sup>leu</sup>. First, ATP and leucine are bound and AMP is transfered to the backbone carboxylic acid of leucine with the release of a pyrophosphate. Second, tRNA<sup>leu</sup> is bound with the leucyl adenylate and leucine is transfered to either the 2' OH of the 3' terminal adenine with the release of AMP<ref>doi: 10.1038/nsmb.2317</ref>.		The <scene name='78/786656/Catalytic/1'>catalytic domain</scene> is responsible for the two step process of charging leucine on to tRNA<sup>leu</sup>. First, ATP and leucine are bound and AMP is transfered to the backbone carboxylic acid of leucine with the release of a pyrophosphate. Second, tRNA<sup>leu</sup> is bound with the leucyl adenylate and leucine is transfered to either the 2' OH of the 3' terminal adenine with the release of AMP<ref>doi: 10.1038/nsmb.2317</ref>.

Christian Fjeld at 13:59, 3 May 2018

Christian Fjeld — Thu, 03 May 2018 13:59:46 GMT

←Older revision		Revision as of 13:59, 3 May 2018
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	=== Catalytic Domain ===		=== Catalytic Domain ===
-		+	[[Image:CatalyticSite.png \| thumb]]
	The <scene name='78/786656/Catalytic/1'>catalytic domain</scene> is responsible for the two step process of charging leucine on to tRNA<sup>leu</sup>. First, ATP and leucine are bound and AMP is transfered to the backbone carboxylic acid of leucine with the release of a pyrophosphate. Second, tRNA<sup>leu</sup> is bound with the leucyl adenylate and leucine is transfered to either the 2' OH of the 3' terminal adenine with the release of AMP<ref>doi: 10.1038/nsmb.2317</ref>.		The <scene name='78/786656/Catalytic/1'>catalytic domain</scene> is responsible for the two step process of charging leucine on to tRNA<sup>leu</sup>. First, ATP and leucine are bound and AMP is transfered to the backbone carboxylic acid of leucine with the release of a pyrophosphate. Second, tRNA<sup>leu</sup> is bound with the leucyl adenylate and leucine is transfered to either the 2' OH of the 3' terminal adenine with the release of AMP<ref>doi: 10.1038/nsmb.2317</ref>.

Christian Fjeld at 13:48, 3 May 2018

Christian Fjeld — Thu, 03 May 2018 13:48:49 GMT

←Older revision		Revision as of 13:48, 3 May 2018
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	The <scene name='78/786656/Editing/1'>editing domain</scene> of LARS is responsible for hydrolysing mischarged tRNA, such as ile-tRNA<sup>leu</sup>, and releasing it for a subsequent round of aminoacylation. This editing function allows cells to achieve a tRNA charging error rate of less than 1:10,000<ref>doi: 10.1016/j.jmb.2009.04.073</ref>. The domain itself is an β sandwich connected to the catalytic domain by a flexible loop that allows a hinge action to bind aminoacylated tRNAs for error checking.		The <scene name='78/786656/Editing/1'>editing domain</scene> of LARS is responsible for hydrolysing mischarged tRNA, such as ile-tRNA<sup>leu</sup>, and releasing it for a subsequent round of aminoacylation. This editing function allows cells to achieve a tRNA charging error rate of less than 1:10,000<ref>doi: 10.1016/j.jmb.2009.04.073</ref>. The domain itself is an β sandwich connected to the catalytic domain by a flexible loop that allows a hinge action to bind aminoacylated tRNAs for error checking.

-	[[Image:~~Editing~~.JPG]]	+	[[Image:Editing2.JPG]]

	The binding pocket of the editing domain acts as a reciprocal sieve to the catalytic domain. The catalytic domain cannot distinguish between amino acids that are similar to, or smaller than leucine. The binding pocket of the editing site can accommodate these similar or smaller amino acids but excludes leucine due to a steric clash with a highly conserved theronine<ref>doi: 10.1016/j.jmb.2009.04.073</ref>. Together, the catalytic site discriminates against larger or hydrophobically different amino acids and the editing site hydrolyzes smaller, structurally similar amino acids producing a very low error rate<ref>DOI: 10.1042/BJ20051249</ref>.		The binding pocket of the editing domain acts as a reciprocal sieve to the catalytic domain. The catalytic domain cannot distinguish between amino acids that are similar to, or smaller than leucine. The binding pocket of the editing site can accommodate these similar or smaller amino acids but excludes leucine due to a steric clash with a highly conserved theronine<ref>doi: 10.1016/j.jmb.2009.04.073</ref>. Together, the catalytic site discriminates against larger or hydrophobically different amino acids and the editing site hydrolyzes smaller, structurally similar amino acids producing a very low error rate<ref>DOI: 10.1042/BJ20051249</ref>.

Christian Fjeld at 13:47, 3 May 2018

Christian Fjeld — Thu, 03 May 2018 13:47:45 GMT

←Older revision		Revision as of 13:47, 3 May 2018
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	The <scene name='78/786656/Catalytic/1'>catalytic domain</scene> is responsible for the two step process of charging leucine on to tRNA<sup>leu</sup>. First, ATP and leucine are bound and AMP is transfered to the backbone carboxylic acid of leucine with the release of a pyrophosphate. Second, tRNA<sup>leu</sup> is bound with the leucyl adenylate and leucine is transfered to either the 2' OH of the 3' terminal adenine with the release of AMP<ref>doi: 10.1038/nsmb.2317</ref>.		The <scene name='78/786656/Catalytic/1'>catalytic domain</scene> is responsible for the two step process of charging leucine on to tRNA<sup>leu</sup>. First, ATP and leucine are bound and AMP is transfered to the backbone carboxylic acid of leucine with the release of a pyrophosphate. Second, tRNA<sup>leu</sup> is bound with the leucyl adenylate and leucine is transfered to either the 2' OH of the 3' terminal adenine with the release of AMP<ref>doi: 10.1038/nsmb.2317</ref>.

-	[[Image:~~Scheme~~.JPG]]	+	[[Image:Scheme2.JPG]]

	LARS, like all class I synthetases, is characterized by a Rossmann-fold catalytic domain with a central parallel β-sheet with α-helices on both faces. The active site catalyzes both the formation of the leucyl adenylate intermediate and the subsequent charging of leucine onto the terminal acceptor arm of the tRNA<ref>doi: 10.1093/emboj/19.10.2351</ref>. The binding pocket accommodates leucine as well as smaller amino acids such as isoleucine and valine. This allows tRNA<sup>leu</sup> to be mischarged with noncognate amino acids and must be corrected to ensure translational fidelity<ref>doi: 10.1016/S1097-2765(03)00098-4</ref>.		LARS, like all class I synthetases, is characterized by a Rossmann-fold catalytic domain with a central parallel β-sheet with α-helices on both faces. The active site catalyzes both the formation of the leucyl adenylate intermediate and the subsequent charging of leucine onto the terminal acceptor arm of the tRNA<ref>doi: 10.1093/emboj/19.10.2351</ref>. The binding pocket accommodates leucine as well as smaller amino acids such as isoleucine and valine. This allows tRNA<sup>leu</sup> to be mischarged with noncognate amino acids and must be corrected to ensure translational fidelity<ref>doi: 10.1016/S1097-2765(03)00098-4</ref>.
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	The <scene name='78/786656/Editing/1'>editing domain</scene> of LARS is responsible for hydrolysing mischarged tRNA, such as ile-tRNA<sup>leu</sup>, and releasing it for a subsequent round of aminoacylation. This editing function allows cells to achieve a tRNA charging error rate of less than 1:10,000<ref>doi: 10.1016/j.jmb.2009.04.073</ref>. The domain itself is an β sandwich connected to the catalytic domain by a flexible loop that allows a hinge action to bind aminoacylated tRNAs for error checking.		The <scene name='78/786656/Editing/1'>editing domain</scene> of LARS is responsible for hydrolysing mischarged tRNA, such as ile-tRNA<sup>leu</sup>, and releasing it for a subsequent round of aminoacylation. This editing function allows cells to achieve a tRNA charging error rate of less than 1:10,000<ref>doi: 10.1016/j.jmb.2009.04.073</ref>. The domain itself is an β sandwich connected to the catalytic domain by a flexible loop that allows a hinge action to bind aminoacylated tRNAs for error checking.
		+
		+	[[Image:Editing.JPG]]

	The binding pocket of the editing domain acts as a reciprocal sieve to the catalytic domain. The catalytic domain cannot distinguish between amino acids that are similar to, or smaller than leucine. The binding pocket of the editing site can accommodate these similar or smaller amino acids but excludes leucine due to a steric clash with a highly conserved theronine<ref>doi: 10.1016/j.jmb.2009.04.073</ref>. Together, the catalytic site discriminates against larger or hydrophobically different amino acids and the editing site hydrolyzes smaller, structurally similar amino acids producing a very low error rate<ref>DOI: 10.1042/BJ20051249</ref>.		The binding pocket of the editing domain acts as a reciprocal sieve to the catalytic domain. The catalytic domain cannot distinguish between amino acids that are similar to, or smaller than leucine. The binding pocket of the editing site can accommodate these similar or smaller amino acids but excludes leucine due to a steric clash with a highly conserved theronine<ref>doi: 10.1016/j.jmb.2009.04.073</ref>. Together, the catalytic site discriminates against larger or hydrophobically different amino acids and the editing site hydrolyzes smaller, structurally similar amino acids producing a very low error rate<ref>DOI: 10.1042/BJ20051249</ref>.

Christian Fjeld at 13:37, 3 May 2018

Christian Fjeld — Thu, 03 May 2018 13:37:18 GMT

←Older revision		Revision as of 13:37, 3 May 2018
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	== Structure ==		== Structure ==

-	LARS is composed of five domains, two catalyticly active domains; the catalytic and editing domains, one tRNA recognition domain; the anticodon binding domain, and two domains that pivot over the aminoacylation site; the leucine-specific and zinc binding domains.	+	LARS is composed of five domains, two catalyticly active domains; the catalytic and editing domains, one tRNA recognition domain; the anticodon binding domain, and two domains that pivot over the aminoacylation site; the leucine-specific and zinc binding domains. Together, these five domains carry out the task of aminoacylating uncharged tRNA and hydrolysing mischarged tRNA with a high specificity for tRNA<sup>leu</sup>.

	=== Catalytic Domain ===		=== Catalytic Domain ===

Christian Fjeld at 13:34, 3 May 2018

Christian Fjeld — Thu, 03 May 2018 13:34:11 GMT

←Older revision		Revision as of 13:34, 3 May 2018
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	== Structure ==		== Structure ==
		+
		+	LARS is composed of five domains, two catalyticly active domains; the catalytic and editing domains, one tRNA recognition domain; the anticodon binding domain, and two domains that pivot over the aminoacylation site; the leucine-specific and zinc binding domains.

	=== Catalytic Domain ===		=== Catalytic Domain ===
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	=== Zinc Binding Domain ===		=== Zinc Binding Domain ===

-	The <scene name='78/786656/Zn1/1'>zinc binding domain</scene> is a highly variable domain and different species have have 0-2 zinc binding motifs within the domain<ref>doi: 10.1093/emboj/19.10.2351</ref>. It is highly disordered in the apo state and, similar to the leucine-specific domain, closes and interacts with the tRNA in the aminoacylation state. It is unclear if the zinc ligand actively participates in catalysis or is required for the correct folding of the domain ~~and may vary by species~~. Mutation of the zinc binding motif in some species, ''E. coli'', produces an inactive enzyme<ref>doi: 10.1093/emboj/19.10.2351</ref>.	+	The <scene name='78/786656/Zn1/1'>zinc binding domain</scene> is a highly variable domain and different species have have 0-2 zinc binding motifs within the domain<ref>doi: 10.1093/emboj/19.10.2351</ref>. It is highly disordered in the apo state and, similar to the leucine-specific domain, closes and interacts with the tRNA in the aminoacylation state. It is unclear if the zinc ligand actively participates in catalysis or is required for the correct folding of the domain. Mutation of the zinc binding motif in some species, ''E. coli'', produces an inactive enzyme<ref>doi: 10.1093/emboj/19.10.2351</ref>.