4f56

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:30, 17 October 2024) (edit) (undo)
 
(4 intermediate revisions not shown.)
Line 1: Line 1:
 +
==The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5==
==The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5==
-
<StructureSection load='4f56' size='340' side='right' caption='[[4f56]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+
<StructureSection load='4f56' size='340' side='right'caption='[[4f56]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4f56]] is a 4 chain structure with sequence 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=4F56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4F56 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4f56]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F56 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGK:3-[(2R,3AR,5R,6R,6AR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-2,6-DIHYDROXYTETRAHYDROFURO[2,3-D][1,3]OXATHIOL-2-YL]PROPANOIC+ACID'>CGK</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4f4u|4f4u]], [[3riy|3riy]], [[3rig|3rig]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CGK:3-[(2R,3aR,5R,6R,6aR)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,6-bis(oxidanyl)-3a,5,6,6a-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]propanoic+acid'>CGK</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SIR2L5, SIRT5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4f56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f56 OCA], [https://pdbe.org/4f56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f56 RCSB], [https://www.ebi.ac.uk/pdbsum/4f56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f56 ProSAT]</span></td></tr>
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4f56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f56 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4f56 RCSB], [http://www.ebi.ac.uk/pdbsum/4f56 PDBsum]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/SIRT5_HUMAN SIRT5_HUMAN]] NAD-dependent lysine demalonylase and desuccinylase that specifically removes malonyl and succinyl groups on target proteins. Activates CPS1 and contributes to the regulation of blood ammonia levels during prolonged fasting: acts by mediating desuccinylation of CPS1, thereby increasing CPS1 activity in response to elevated NAD levels during fasting. Has weak NAD-dependent protein deacetylase activity; however this activity may not be physiologically relevant in vivo. Can deacetylate cytochrome c (CYCS) and a number of other proteins in vitro.<ref>PMID:18680753</ref> <ref>PMID:21908771</ref> <ref>PMID:22076378</ref>
+
[https://www.uniprot.org/uniprot/SIR5_HUMAN SIR5_HUMAN] NAD-dependent lysine demalonylase and desuccinylase that specifically removes malonyl and succinyl groups on target proteins. Activates CPS1 and contributes to the regulation of blood ammonia levels during prolonged fasting: acts by mediating desuccinylation of CPS1, thereby increasing CPS1 activity in response to elevated NAD levels during fasting. Activates SOD1 by mediating its desuccinylation, leading to reduced reactive oxygen species. Has weak NAD-dependent protein deacetylase activity; however this activity may not be physiologically relevant in vivo. Can deacetylate cytochrome c (CYCS) and a number of other proteins in vitro.<ref>PMID:18680753</ref> <ref>PMID:21908771</ref> <ref>PMID:24140062</ref> <ref>PMID:22076378</ref>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
Line 18: Line 18:
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
 +
<div class="pdbe-citations 4f56" style="background-color:#fffaf0;"></div>
 +
 +
==See Also==
 +
*[[Histone deacetylase 3D structures|Histone deacetylase 3D structures]]
== References ==
== References ==
<references/>
<references/>
Line 23: Line 27:
</StructureSection>
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Hao, Q]]
+
[[Category: Large Structures]]
-
[[Category: Zhou, Y]]
+
[[Category: Hao Q]]
-
[[Category: Hydrolase]]
+
[[Category: Zhou Y]]
-
[[Category: Mitochondrial sirtuin]]
+
-
[[Category: Nad-dependent demalonylase and desuccinylase]]
+
-
[[Category: Rossmann fold domain]]
+
-
[[Category: Zn-binding domain]]
+

Current revision

The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5

PDB ID 4f56

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4f56"
Personal tools