2bfq: Difference between revisions

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[[Image:2bfq.png|left|200px]]


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==MACRO DOMAINS ARE ADP-RIBOSE BINDING MOLECULES==
The line below this paragraph, containing "STRUCTURE_2bfq", creates the "Structure Box" on the page.
<StructureSection load='2bfq' size='340' side='right'caption='[[2bfq]], [[Resolution|resolution]] 1.50&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'>[[2bfq]] 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=2BFQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BFQ 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]] 1.5&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AR6:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL]+HYDROGEN+PHOSPHATE'>AR6</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>
{{STRUCTURE_2bfq|  PDB=2bfq  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bfq OCA], [https://pdbe.org/2bfq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bfq RCSB], [https://www.ebi.ac.uk/pdbsum/2bfq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bfq ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Y1521_ARCFU Y1521_ARCFU] Removes ADP-ribose from glutamate residues in proteins bearing a single ADP-ribose moiety. Inactive towards proteins bearing poly-ADP-ribose. Catalyzes removal of a phosphate group from ADP-ribose 1''-phosphate (Appr1p), but with low efficiency.<ref>PMID:23474712</ref> <ref>PMID:15902274</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/bf/2bfq_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2bfq ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The ADP-ribosylation of proteins is an important post-translational modification that occurs in a variety of biological processes, including DNA repair, transcription, chromatin biology and long-term memory formation. Yet no protein modules are known that specifically recognize the ADP-ribose nucleotide. We provide biochemical and structural evidence that macro domains are high-affinity ADP-ribose binding modules. Our structural analysis reveals a conserved ligand binding pocket among the macro domain fold. Consistently, distinct human macro domains retain their ability to bind ADP-ribose. In addition, some macro domain proteins also recognize poly-ADP-ribose as a ligand. Our data suggest an important role for proteins containing macro domains in the biology of ADP-ribose.


===MACRO DOMAINS ARE ADP-RIBOSE BINDING MOLECULES===
The macro domain is an ADP-ribose binding module.,Karras GI, Kustatscher G, Buhecha HR, Allen MD, Pugieux C, Sait F, Bycroft M, Ladurner AG EMBO J. 2005 Jun 1;24(11):1911-20. Epub 2005 May 19. PMID:15902274<ref>PMID:15902274</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_15902274}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2bfq" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 15902274 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_15902274}}
__TOC__
 
</StructureSection>
==About this Structure==
[[2bfq]] is a 1 chain structure with 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=2BFQ OCA].
 
==Reference==
<ref group="xtra">PMID:015902274</ref><ref group="xtra">PMID:015965484</ref><references group="xtra"/>
[[Category: Archaeoglobus fulgidus]]
[[Category: Archaeoglobus fulgidus]]
[[Category: Allen, M D.]]
[[Category: Large Structures]]
[[Category: Buhecha, H R.]]
[[Category: Allen MD]]
[[Category: Bycroft, M.]]
[[Category: Buhecha HR]]
[[Category: Karras, G I.]]
[[Category: Bycroft M]]
[[Category: Ladurner, A G.]]
[[Category: Karras GI]]
[[Category: Pugieux, C.]]
[[Category: Ladurner AG]]
[[Category: Sait, F.]]
[[Category: Pugieux C]]
[[Category: Adp ribose-binding protein]]
[[Category: Sait F]]
[[Category: Histone macroh2a]]
[[Category: Hydrolase]]
[[Category: Macro_h2a domain]]
[[Category: Nucleotide]]
[[Category: P-loop]]

Latest revision as of 10:46, 23 October 2024

MACRO DOMAINS ARE ADP-RIBOSE BINDING MOLECULESMACRO DOMAINS ARE ADP-RIBOSE BINDING MOLECULES

Structural highlights

2bfq 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 1.5Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Y1521_ARCFU Removes ADP-ribose from glutamate residues in proteins bearing a single ADP-ribose moiety. Inactive towards proteins bearing poly-ADP-ribose. Catalyzes removal of a phosphate group from ADP-ribose 1-phosphate (Appr1p), but with low efficiency.[1] [2]

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 ADP-ribosylation of proteins is an important post-translational modification that occurs in a variety of biological processes, including DNA repair, transcription, chromatin biology and long-term memory formation. Yet no protein modules are known that specifically recognize the ADP-ribose nucleotide. We provide biochemical and structural evidence that macro domains are high-affinity ADP-ribose binding modules. Our structural analysis reveals a conserved ligand binding pocket among the macro domain fold. Consistently, distinct human macro domains retain their ability to bind ADP-ribose. In addition, some macro domain proteins also recognize poly-ADP-ribose as a ligand. Our data suggest an important role for proteins containing macro domains in the biology of ADP-ribose.

The macro domain is an ADP-ribose binding module.,Karras GI, Kustatscher G, Buhecha HR, Allen MD, Pugieux C, Sait F, Bycroft M, Ladurner AG EMBO J. 2005 Jun 1;24(11):1911-20. Epub 2005 May 19. PMID:15902274[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Jankevicius G, Hassler M, Golia B, Rybin V, Zacharias M, Timinszky G, Ladurner AG. A family of macrodomain proteins reverses cellular mono-ADP-ribosylation. Nat Struct Mol Biol. 2013 Apr;20(4):508-14. doi: 10.1038/nsmb.2523. Epub 2013 Mar, 10. PMID:23474712 doi:http://dx.doi.org/10.1038/nsmb.2523
  2. ↑ Karras GI, Kustatscher G, Buhecha HR, Allen MD, Pugieux C, Sait F, Bycroft M, Ladurner AG. The macro domain is an ADP-ribose binding module. EMBO J. 2005 Jun 1;24(11):1911-20. Epub 2005 May 19. PMID:15902274
  3. ↑ Karras GI, Kustatscher G, Buhecha HR, Allen MD, Pugieux C, Sait F, Bycroft M, Ladurner AG. The macro domain is an ADP-ribose binding module. EMBO J. 2005 Jun 1;24(11):1911-20. Epub 2005 May 19. PMID:15902274

2bfq, resolution 1.50Å

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