Human SUMO E1 complex - Revision history

Alexander Berchansky at 10:45, 16 May 2017

Alexander Berchansky — Tue, 16 May 2017 10:45:46 GMT

←Older revision		Revision as of 10:45, 16 May 2017
Line 1:		Line 1:
-	<StructureSection load='3kyc' size=~~'500' frame~~=~~'true' side~~=~~'right' scene~~= caption='Human SUMO-activating enzyme subunits 1 & 2 complex with SUMO-1, deoxy-sulfamoylamino-adenosine and Zn+2 ion [[3kyc]]' >	+	<StructureSection load='3kyc' size="400" color="" spin="on" Scene= caption='Human SUMO-activating enzyme subunits 1 & 2 complex with SUMO-1, deoxy-sulfamoylamino-adenosine and Zn+2 ion [[3kyc]] >

	Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins attached to their target proteins and modulating the activities of those targets in various ways. Three types of evolutionarily conserved enzymes — E1 activating enzymes, E2 conjugating enzymes and E3 ligase enzymes — act sequentially through parallel yet distinct pathways to conjugate ubiquitin and Ubl proteins, such as SUMO and NEDD8, to their targets. The E1 enzyme uses the <scene name='3kyc/Cv/3'>adenosine triphosphate (ATP)</scene> and magnesium to adenylate the C-terminal Ub/Ubl glycine, releasing pyrophosphate and resulting in <scene name='3kyc/Cv/8'>adenosine monophosphate (AMP)</scene>. A non-hydrolysable <scene name='3kyc/Cv/4'>mimic of the acyl adenylate intermediate (AMSN)</scene> and <scene name='3kyc/Cv/5'>mimic of the tetrahedral intermediate (AVSN)</scene> were constructed. In both these compounds the atom of <font color='orange'><b>phosphorus</b></font> is replaced by sulfur (colored <span style="color:yellow;background-color:black;font-weight:bold;">yellow</span>).		Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins attached to their target proteins and modulating the activities of those targets in various ways. Three types of evolutionarily conserved enzymes — E1 activating enzymes, E2 conjugating enzymes and E3 ligase enzymes — act sequentially through parallel yet distinct pathways to conjugate ubiquitin and Ubl proteins, such as SUMO and NEDD8, to their targets. The E1 enzyme uses the <scene name='3kyc/Cv/3'>adenosine triphosphate (ATP)</scene> and magnesium to adenylate the C-terminal Ub/Ubl glycine, releasing pyrophosphate and resulting in <scene name='3kyc/Cv/8'>adenosine monophosphate (AMP)</scene>. A non-hydrolysable <scene name='3kyc/Cv/4'>mimic of the acyl adenylate intermediate (AMSN)</scene> and <scene name='3kyc/Cv/5'>mimic of the tetrahedral intermediate (AVSN)</scene> were constructed. In both these compounds the atom of <font color='orange'><b>phosphorus</b></font> is replaced by sulfur (colored <span style="color:yellow;background-color:black;font-weight:bold;">yellow</span>).
-

	The <scene name='3kyc/Al/2'>structural alignment</scene> of the crystal structures for human SUMO E1 in complex with SUMO adenylate (AMSN) and tetrahedral intermediate (AVSN) analogues revealed opened conformation (<font color='orange'><b>SUMO1 in orange</b></font>, <font color='blue'><b>SAE1 colored in blue</b></font>, and <font color='darkviolet'><b>other domains in darkviolet</b></font>) and closed conformation (<span style="color:yellow;background-color:black;font-weight:bold;">SUMO1 in yellow</span>, <font color='cyan'><b>SAE1 colored in cyan</b></font>, and <font color='magenta'><b>other domains in magenta</b></font>), respectively. In the <scene name='3kyc/Al/7'>open conformation</scene> ([[3kyc]]) the distance between Cys domain (including Cys173) and mimic of the acyl adenylate intermediate AMSN is very long, while in the <scene name='3kyc/Al/6'>closed conformation</scene> ([[3kyd]]), the catalytic Cys173 is posioned near AVSN and SUMO1, so the overall structure revealed dramatic rearrangement. This large conformational change forms the <scene name='3kyc/Al/8'>E1~SUMO1-AVSN tetrahedral intermediate analogue</scene>.		The <scene name='3kyc/Al/2'>structural alignment</scene> of the crystal structures for human SUMO E1 in complex with SUMO adenylate (AMSN) and tetrahedral intermediate (AVSN) analogues revealed opened conformation (<font color='orange'><b>SUMO1 in orange</b></font>, <font color='blue'><b>SAE1 colored in blue</b></font>, and <font color='darkviolet'><b>other domains in darkviolet</b></font>) and closed conformation (<span style="color:yellow;background-color:black;font-weight:bold;">SUMO1 in yellow</span>, <font color='cyan'><b>SAE1 colored in cyan</b></font>, and <font color='magenta'><b>other domains in magenta</b></font>), respectively. In the <scene name='3kyc/Al/7'>open conformation</scene> ([[3kyc]]) the distance between Cys domain (including Cys173) and mimic of the acyl adenylate intermediate AMSN is very long, while in the <scene name='3kyc/Al/6'>closed conformation</scene> ([[3kyd]]), the catalytic Cys173 is posioned near AVSN and SUMO1, so the overall structure revealed dramatic rearrangement. This large conformational change forms the <scene name='3kyc/Al/8'>E1~SUMO1-AVSN tetrahedral intermediate analogue</scene>.

Alexander Berchansky at 10:42, 16 May 2017

Alexander Berchansky — Tue, 16 May 2017 10:42:58 GMT

←Older revision		Revision as of 10:42, 16 May 2017
Line 1:		Line 1:
-	<StructureSection load='3kyc' size='500' frame='true' ~~align~~='right' scene= caption='Human SUMO-activating enzyme subunits 1 & 2 complex with SUMO-1, deoxy-sulfamoylamino-adenosine and Zn+2 ion [[3kyc]]' >	+	<StructureSection load='3kyc' size='500' frame='true' side='right' scene= caption='Human SUMO-activating enzyme subunits 1 & 2 complex with SUMO-1, deoxy-sulfamoylamino-adenosine and Zn+2 ion [[3kyc]]' >
-		+
-		+

	Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins attached to their target proteins and modulating the activities of those targets in various ways. Three types of evolutionarily conserved enzymes — E1 activating enzymes, E2 conjugating enzymes and E3 ligase enzymes — act sequentially through parallel yet distinct pathways to conjugate ubiquitin and Ubl proteins, such as SUMO and NEDD8, to their targets. The E1 enzyme uses the <scene name='3kyc/Cv/3'>adenosine triphosphate (ATP)</scene> and magnesium to adenylate the C-terminal Ub/Ubl glycine, releasing pyrophosphate and resulting in <scene name='3kyc/Cv/8'>adenosine monophosphate (AMP)</scene>. A non-hydrolysable <scene name='3kyc/Cv/4'>mimic of the acyl adenylate intermediate (AMSN)</scene> and <scene name='3kyc/Cv/5'>mimic of the tetrahedral intermediate (AVSN)</scene> were constructed. In both these compounds the atom of <font color='orange'><b>phosphorus</b></font> is replaced by sulfur (colored <span style="color:yellow;background-color:black;font-weight:bold;">yellow</span>).		Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins attached to their target proteins and modulating the activities of those targets in various ways. Three types of evolutionarily conserved enzymes — E1 activating enzymes, E2 conjugating enzymes and E3 ligase enzymes — act sequentially through parallel yet distinct pathways to conjugate ubiquitin and Ubl proteins, such as SUMO and NEDD8, to their targets. The E1 enzyme uses the <scene name='3kyc/Cv/3'>adenosine triphosphate (ATP)</scene> and magnesium to adenylate the C-terminal Ub/Ubl glycine, releasing pyrophosphate and resulting in <scene name='3kyc/Cv/8'>adenosine monophosphate (AMP)</scene>. A non-hydrolysable <scene name='3kyc/Cv/4'>mimic of the acyl adenylate intermediate (AMSN)</scene> and <scene name='3kyc/Cv/5'>mimic of the tetrahedral intermediate (AVSN)</scene> were constructed. In both these compounds the atom of <font color='orange'><b>phosphorus</b></font> is replaced by sulfur (colored <span style="color:yellow;background-color:black;font-weight:bold;">yellow</span>).

Michal Harel at 16:27, 13 January 2012

Michal Harel — Fri, 13 Jan 2012 16:27:55 GMT

←Older revision		Revision as of 16:27, 13 January 2012
Line 13:		Line 13:
	[[Image:kyc.gif\|left\|500px]]		[[Image:kyc.gif\|left\|500px]]
	For better understanding of the difference between these two conformations you can see this [[Morphs\|morph]] (generated by using [http://polyview.cchmc.org/polyview3d.html POLYVIEW-3D: http://polyview.cchmc.org/polyview3d.html]; reload/refresh this page to restart this movie). Of note, in contrast to the previous figure, the same domains of these two structures ([[3kyc]] and [[3kyd]]) are colored in the same colors (<span style="color:yellow;background-color:black;font-weight:bold;">SUMO1 in yellow</span>, <font color='blue'><b>SAE1 colored in blue</b></font> and <font color='darkviolet'><b>other domains in darkviolet</b></font>). The catalytic Cys173 is shown in the spacefill representation and colored green, AMSN (or AVSN) are shown in the spacefill representation and colored in CPK colors.		For better understanding of the difference between these two conformations you can see this [[Morphs\|morph]] (generated by using [http://polyview.cchmc.org/polyview3d.html POLYVIEW-3D: http://polyview.cchmc.org/polyview3d.html]; reload/refresh this page to restart this movie). Of note, in contrast to the previous figure, the same domains of these two structures ([[3kyc]] and [[3kyd]]) are colored in the same colors (<span style="color:yellow;background-color:black;font-weight:bold;">SUMO1 in yellow</span>, <font color='blue'><b>SAE1 colored in blue</b></font> and <font color='darkviolet'><b>other domains in darkviolet</b></font>). The catalytic Cys173 is shown in the spacefill representation and colored green, AMSN (or AVSN) are shown in the spacefill representation and colored in CPK colors.
-	{{Clear}}	+	{{Clear}}
		+
		+	==3D structures of SUMO==
		+
		+	[[SUMO]]

Michal Harel at 16:24, 13 January 2012

Michal Harel — Fri, 13 Jan 2012 16:24:16 GMT

←Older revision		Revision as of 16:24, 13 January 2012
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-	<StructureSection load='3kyc' size='500' frame='true' align='right' scene= caption='[[3kyc]]' >	+	<StructureSection load='3kyc' size='500' frame='true' align='right' scene= caption='Human SUMO-activating enzyme subunits 1 & 2 complex with SUMO-1, deoxy-sulfamoylamino-adenosine and Zn+2 ion [[3kyc]]' >

Michal Harel at 16:21, 13 January 2012

Michal Harel — Fri, 13 Jan 2012 16:21:38 GMT

←Older revision		Revision as of 16:21, 13 January 2012
Line 1:		Line 1:
-	<StructureSection load='3kyc' size='500' frame='true' align='right' scene='3kyc/Cv/1' caption='[[3kyc]]' >
-
	<StructureSection load='3kyc' size='500' frame='true' align='right' scene= caption='[[3kyc]]' >		<StructureSection load='3kyc' size='500' frame='true' align='right' scene= caption='[[3kyc]]' >

Michal Harel at 16:20, 13 January 2012

Michal Harel — Fri, 13 Jan 2012 16:20:08 GMT

←Older revision		Revision as of 16:20, 13 January 2012
Line 1:		Line 1:
	<StructureSection load='3kyc' size='500' frame='true' align='right' scene='3kyc/Cv/1' caption='[[3kyc]]' >		<StructureSection load='3kyc' size='500' frame='true' align='right' scene='3kyc/Cv/1' caption='[[3kyc]]' >
		+
		+	<StructureSection load='3kyc' size='500' frame='true' align='right' scene= caption='[[3kyc]]' >
		+
		+

	Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins attached to their target proteins and modulating the activities of those targets in various ways. Three types of evolutionarily conserved enzymes — E1 activating enzymes, E2 conjugating enzymes and E3 ligase enzymes — act sequentially through parallel yet distinct pathways to conjugate ubiquitin and Ubl proteins, such as SUMO and NEDD8, to their targets. The E1 enzyme uses the <scene name='3kyc/Cv/3'>adenosine triphosphate (ATP)</scene> and magnesium to adenylate the C-terminal Ub/Ubl glycine, releasing pyrophosphate and resulting in <scene name='3kyc/Cv/8'>adenosine monophosphate (AMP)</scene>. A non-hydrolysable <scene name='3kyc/Cv/4'>mimic of the acyl adenylate intermediate (AMSN)</scene> and <scene name='3kyc/Cv/5'>mimic of the tetrahedral intermediate (AVSN)</scene> were constructed. In both these compounds the atom of <font color='orange'><b>phosphorus</b></font> is replaced by sulfur (colored <span style="color:yellow;background-color:black;font-weight:bold;">yellow</span>).		Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins attached to their target proteins and modulating the activities of those targets in various ways. Three types of evolutionarily conserved enzymes — E1 activating enzymes, E2 conjugating enzymes and E3 ligase enzymes — act sequentially through parallel yet distinct pathways to conjugate ubiquitin and Ubl proteins, such as SUMO and NEDD8, to their targets. The E1 enzyme uses the <scene name='3kyc/Cv/3'>adenosine triphosphate (ATP)</scene> and magnesium to adenylate the C-terminal Ub/Ubl glycine, releasing pyrophosphate and resulting in <scene name='3kyc/Cv/8'>adenosine monophosphate (AMP)</scene>. A non-hydrolysable <scene name='3kyc/Cv/4'>mimic of the acyl adenylate intermediate (AMSN)</scene> and <scene name='3kyc/Cv/5'>mimic of the tetrahedral intermediate (AVSN)</scene> were constructed. In both these compounds the atom of <font color='orange'><b>phosphorus</b></font> is replaced by sulfur (colored <span style="color:yellow;background-color:black;font-weight:bold;">yellow</span>).

Michal Harel at 16:16, 13 January 2012

Michal Harel — Fri, 13 Jan 2012 16:16:16 GMT

←Older revision		Revision as of 16:16, 13 January 2012
Line 1:		Line 1:
-	<StructureSection load='3kyc' size='500' frame='true' align='right' scene='3kyc/Cv/1' >	+	<StructureSection load='3kyc' size='500' frame='true' align='right' scene='3kyc/Cv/1' caption='[[3kyc]]' >

	Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins attached to their target proteins and modulating the activities of those targets in various ways. Three types of evolutionarily conserved enzymes — E1 activating enzymes, E2 conjugating enzymes and E3 ligase enzymes — act sequentially through parallel yet distinct pathways to conjugate ubiquitin and Ubl proteins, such as SUMO and NEDD8, to their targets. The E1 enzyme uses the <scene name='3kyc/Cv/3'>adenosine triphosphate (ATP)</scene> and magnesium to adenylate the C-terminal Ub/Ubl glycine, releasing pyrophosphate and resulting in <scene name='3kyc/Cv/8'>adenosine monophosphate (AMP)</scene>. A non-hydrolysable <scene name='3kyc/Cv/4'>mimic of the acyl adenylate intermediate (AMSN)</scene> and <scene name='3kyc/Cv/5'>mimic of the tetrahedral intermediate (AVSN)</scene> were constructed. In both these compounds the atom of <font color='orange'><b>phosphorus</b></font> is replaced by sulfur (colored <span style="color:yellow;background-color:black;font-weight:bold;">yellow</span>).		Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins attached to their target proteins and modulating the activities of those targets in various ways. Three types of evolutionarily conserved enzymes — E1 activating enzymes, E2 conjugating enzymes and E3 ligase enzymes — act sequentially through parallel yet distinct pathways to conjugate ubiquitin and Ubl proteins, such as SUMO and NEDD8, to their targets. The E1 enzyme uses the <scene name='3kyc/Cv/3'>adenosine triphosphate (ATP)</scene> and magnesium to adenylate the C-terminal Ub/Ubl glycine, releasing pyrophosphate and resulting in <scene name='3kyc/Cv/8'>adenosine monophosphate (AMP)</scene>. A non-hydrolysable <scene name='3kyc/Cv/4'>mimic of the acyl adenylate intermediate (AMSN)</scene> and <scene name='3kyc/Cv/5'>mimic of the tetrahedral intermediate (AVSN)</scene> were constructed. In both these compounds the atom of <font color='orange'><b>phosphorus</b></font> is replaced by sulfur (colored <span style="color:yellow;background-color:black;font-weight:bold;">yellow</span>).

Alexander Berchansky at 08:56, 12 May 2011

Alexander Berchansky — Thu, 12 May 2011 08:56:09 GMT

←Older revision		Revision as of 08:56, 12 May 2011
Line 13:		Line 13:
	{{Clear}}		{{Clear}}

-
-	==About this Structure==
-	3KYD is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYD OCA].

	==Reference==		==Reference==

Alexander Berchansky: New page: Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins attached to their target proteins and modulating t...

Alexander Berchansky — Thu, 12 May 2011 08:55:24 GMT

New page: <StructureSection load='3kyc' size='500' frame='true' align='right' scene='3kyc/Cv/1' > Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins attached to their target proteins and modulating t...

New page

<StructureSection load='3kyc' size='500' frame='true' align='right' scene='3kyc/Cv/1' >

Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins attached to their target proteins and modulating the activities of those targets in various ways. Three types of evolutionarily conserved enzymes — E1 activating enzymes, E2 conjugating enzymes and E3 ligase enzymes — act sequentially through parallel yet distinct pathways to conjugate ubiquitin and Ubl proteins, such as SUMO and NEDD8, to their targets. The E1 enzyme uses the <scene name='3kyc/Cv/3'>adenosine triphosphate (ATP)</scene> and magnesium to adenylate the C-terminal Ub/Ubl glycine, releasing pyrophosphate and resulting in <scene name='3kyc/Cv/8'>adenosine monophosphate (AMP)</scene>. A non-hydrolysable <scene name='3kyc/Cv/4'>mimic of the acyl adenylate intermediate (AMSN)</scene> and <scene name='3kyc/Cv/5'>mimic of the tetrahedral intermediate (AVSN)</scene> were constructed. In both these compounds the atom of phosphorus is replaced by sulfur (colored yellow).

The <scene name='3kyc/Al/2'>structural alignment</scene> of the crystal structures for human SUMO E1 in complex with SUMO adenylate (AMSN) and tetrahedral intermediate (AVSN) analogues revealed opened conformation (SUMO1 in orange, SAE1 colored in blue, and other domains in darkviolet) and closed conformation (SUMO1 in yellow, SAE1 colored in cyan, and other domains in magenta), respectively. In the <scene name='3kyc/Al/7'>open conformation</scene> ([[3kyc]]) the distance between Cys domain (including Cys173) and mimic of the acyl adenylate intermediate AMSN is very long, while in the <scene name='3kyc/Al/6'>closed conformation</scene> ([[3kyd]]), the catalytic Cys173 is posioned near AVSN and SUMO1, so the overall structure revealed dramatic rearrangement. This large conformational change forms the <scene name='3kyc/Al/8'>E1~SUMO1-AVSN tetrahedral intermediate analogue</scene>.
</StructureSection>

{{Clear}}

[[Image:kyc.gif|left|500px]]
For better understanding of the difference between these two conformations you can see this [[Morphs|morph]] (generated by using [http://polyview.cchmc.org/polyview3d.html POLYVIEW-3D: http://polyview.cchmc.org/polyview3d.html]; reload/refresh this page to restart this movie). Of note, in contrast to the previous figure, the same domains of these two structures ([[3kyc]] and [[3kyd]]) are colored in the same colors (SUMO1 in yellow, SAE1 colored in blue and other domains in darkviolet). The catalytic Cys173 is shown in the spacefill representation and colored green, AMSN (or AVSN) are shown in the spacefill representation and colored in CPK colors.
{{Clear}}

==About this Structure==
3KYD is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYD OCA].

==Reference==
<ref group="xtra">PMID:20164921</ref><references group="xtra"/>
[[Category:Topic Page]]
[[Category: Homo sapiens]]
[[Category: Lima, C D.]]
[[Category: Acetylation]]
[[Category: Adenylation]]
[[Category: Atp-binding]]
[[Category: Cytoplasm]]
[[Category: E1]]
[[Category: Inhibitor]]
[[Category: Isopeptide bond]]
[[Category: Ligase]]
[[Category: Membrane]]
[[Category: Nucleotide-binding]]
[[Category: Nucleus]]
[[Category: Phosphoprotein]]
[[Category: Polymorphism]]
[[Category: Sumo]]
[[Category: Tetrahedral intermediate]]
[[Category: Thioester]]
[[Category: Ubiquitin]]
[[Category: Ubl conjugation pathway]]