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2lgr

From Proteopedia

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Current revision

Solution structure of human protein C6orf130, a putative macro domain

Structural highlights

2lgr is a 1 chain structure with sequence from Homo sapiens. This structure supersedes the now removed PDB entry 2jyc. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OARD1_HUMAN Deacetylates O-acetyl-ADP ribose, a signaling molecule generated by the deacetylation of acetylated lysine residues in histones and other proteins. Catalyzes the deacylation of O-acetyl-ADP-ribose, O-propionyl-ADP-ribose and O-butyryl-ADP-ribose, yielding ADP-ribose plus acetate, propionate and butyrate, respectively.

Publication Abstract from PubMed

Post-translational modification of proteins/histones by lysine acylation has profound effects on the physiological function of modified proteins. Deacylation by NAD(+)-dependent sirtuin reactions yields as a product O-acyl-ADP-ribose, which has been implicated as a signaling molecule in modulating cellular processes. Macrodomain-containing proteins are reported to bind NAD(+)-derived metabolites. Here, we describe the structure and function of an orphan macrodomain protein, human C6orf130. This unique 17-kDa protein is a stand-alone macrodomain protein that occupies a distinct branch in the phylogenic tree. We demonstrate that C6orf130 catalyzes the efficient deacylation of O-acetyl-ADP-ribose, O-propionyl-ADP-ribose, and O-butyryl-ADP-ribose to produce ADP-ribose (ADPr) and acetate, propionate, and butyrate, respectively. Using NMR spectroscopy, we solved the structure of C6orf130 in the presence and absence of ADPr. The structures showed a canonical fold with a deep ligand (ADPr)-binding cleft. Structural comparisons of apo-C6orf130 and the ADPr-C6orf130 complex revealed fluctuations of the beta(5)-alpha(4) loop that covers the bound ADPr, suggesting that the beta(5)-alpha(4) loop functions as a gate to sequester substrate and offer flexibility to accommodate alternative substrates. The ADPr-C6orf130 complex identified amino acid residues involved in substrate binding and suggested residues that function in catalysis. Site-specific mutagenesis and steady-state kinetic analyses revealed two critical catalytic residues, Ser-35 and Asp-125. We propose a catalytic mechanism for deacylation of O-acyl-ADP-ribose by C6orf130 and discuss the biological implications in the context of reversible protein acylation at lysine residues.

Orphan Macrodomain Protein (Human C6orf130) Is an O-Acyl-ADP-ribose Deacylase: SOLUTION STRUCTURE AND CATALYTIC PROPERTIES.,Peterson FC, Chen D, Lytle BL, Rossi MN, Ahel I, Denu JM, Volkman BF J Biol Chem. 2011 Oct 14;286(41):35955-65. Epub 2011 Aug 17. PMID:21849506^[1]

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

References

↑ Peterson FC, Chen D, Lytle BL, Rossi MN, Ahel I, Denu JM, Volkman BF. Orphan Macrodomain Protein (Human C6orf130) Is an O-Acyl-ADP-ribose Deacylase: SOLUTION STRUCTURE AND CATALYTIC PROPERTIES. J Biol Chem. 2011 Oct 14;286(41):35955-65. Epub 2011 Aug 17. PMID:21849506 doi:10.1074/jbc.M111.276238

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2lgr"

Categories: Homo sapiens | Large Structures | Lytle BL | Peterson FC | Volkman BF

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[2lgr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jyc 2jyc]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LGR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LGR FirstGlance]. <br>
-</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=2lgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lgr OCA], [https://pdbe.org/2lgr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lgr RCSB], [https://www.ebi.ac.uk/pdbsum/2lgr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lgr ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2lgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lgr OCA], [https://pdbe.org/2lgr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lgr RCSB], [https://www.ebi.ac.uk/pdbsum/2lgr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lgr ProSAT]</span></td></tr>
 </table>
 == Function ==

2lgr

From Proteopedia

Current revision

Solution structure of human protein C6orf130, a putative macro domain

Structural highlights

Function

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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