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| | <StructureSection load='1m2h' size='340' side='right'caption='[[1m2h]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='1m2h' size='340' side='right'caption='[[1m2h]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1m2h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M2H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1m2h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M2H FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1m2g|1m2g]], [[1m2j|1m2j]], [[1m2k|1m2k]], [[1m2n|1m2n]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1m2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2h OCA], [https://pdbe.org/1m2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m2h RCSB], [https://www.ebi.ac.uk/pdbsum/1m2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2h ProSAT]</span></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=1m2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2h OCA], [https://pdbe.org/1m2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m2h RCSB], [https://www.ebi.ac.uk/pdbsum/1m2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2h ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/NPD1_ARCFU NPD1_ARCFU]] NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form. Deacetylates the N-terminal lysine residue of Alba, the major archaeal chromatin protein and that, in turn, increases Alba's DNA binding affinity, thereby repressing transcription (By similarity).<ref>PMID:10841563</ref>
| + | [https://www.uniprot.org/uniprot/NPD1_ARCFU NPD1_ARCFU] NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form. Deacetylates the N-terminal lysine residue of Alba, the major archaeal chromatin protein and that, in turn, increases Alba's DNA binding affinity, thereby repressing transcription (By similarity).<ref>PMID:10841563</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arcfl]] | + | [[Category: Archaeoglobus fulgidus]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Chang, J]] | + | [[Category: Chang J]] |
| - | [[Category: Cho, Y]] | + | [[Category: Cho Y]] |
| - | [[Category: Gene regulation]]
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| - | [[Category: Protein-ligand complex]]
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| Structural highlights
Function
NPD1_ARCFU NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form. Deacetylates the N-terminal lysine residue of Alba, the major archaeal chromatin protein and that, in turn, increases Alba's DNA binding affinity, thereby repressing transcription (By similarity).[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The NAD-dependent histone/protein deacetylase activity of Sir2 (silent information regulator 2) accounts for its diverse biological roles including gene silencing, DNA damage repair, cell cycle regulation, and life span extension. We provide crystallographic evidence that 2'-O-acetyl ADP-ribose is the reaction product that is formed at the active site of Sir2 from the 2.6-A co-crystal structure of 2'-O-acetyl-ADP-ribose and Sir2 from Archaeoglobus fulgidus. In addition, we show that His-116 and Phe-159 play critical roles in the catalysis and substrate recognition. The conserved Ser-24 and Asp-101 contribute to the stability for NAD binding rather than being directly involved in the catalysis. The crystal structures of wild type and mutant derivatives of Sir2, in conjunction with biochemical analyses of the mutants, provide novel insights into the reaction mechanism of Sir2-mediated deacetylation.
Structural basis for the NAD-dependent deacetylase mechanism of Sir2.,Chang JH, Kim HC, Hwang KY, Lee JW, Jackson SP, Bell SD, Cho Y J Biol Chem. 2002 Sep 13;277(37):34489-98. Epub 2002 Jun 28. PMID:12091395[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Smith JS, Brachmann CB, Celic I, Kenna MA, Muhammad S, Starai VJ, Avalos JL, Escalante-Semerena JC, Grubmeyer C, Wolberger C, Boeke JD. A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family. Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6658-63. PMID:10841563
- ↑ Chang JH, Kim HC, Hwang KY, Lee JW, Jackson SP, Bell SD, Cho Y. Structural basis for the NAD-dependent deacetylase mechanism of Sir2. J Biol Chem. 2002 Sep 13;277(37):34489-98. Epub 2002 Jun 28. PMID:12091395 doi:10.1074/jbc.M205460200
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