1m2h

From Proteopedia

(Difference between revisions)

Current revision

Sir2 homologue S24A mutant-ADP ribose complex

Structural highlights

1m2h is a 1 chain structure with sequence from Archaeoglobus fulgidus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1m2h"

Categories: Archaeoglobus fulgidus | Large Structures | Chang J | Cho Y

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1m2h.png|left|200px]]
-<!--
+==Sir2 homologue S24A mutant-ADP ribose complex==
-The line below this paragraph, containing "STRUCTURE_1m2h", creates the "Structure Box" on the page.
+<StructureSection load='1m2h' size='340' side='right'caption='[[1m2h]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</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>
-{{STRUCTURE_1m2h|  PDB=1m2h  |  SCENE=  }}
+<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>
+== 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>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m2/1m2h_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m2h ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== 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.
-===Sir2 homologue S24A mutant-ADP ribose complex===
+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<ref>PMID:12091395</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_12091395}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1m2h" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12091395 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12091395}}
+__TOC__
+</StructureSection>
-==About this Structure==
-M2H is a [[Single protein]] structure of sequence from [http://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].
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/12091395 12091395]
 [[Category: Archaeoglobus fulgidus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Chang, J.]]
+[[Category: Chang J]]
-[[Category: Cho, Y.]]
+[[Category: Cho Y]]
-[[Category: Protein-ligand complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 23:04:40 2008''

1m2h

From Proteopedia

Current revision

Sir2 homologue S24A mutant-ADP ribose complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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