2ivn

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[[Image:2ivn.jpg|left|200px]]<br /><applet load="2ivn" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2ivn, resolution 1.65&Aring;" />
 
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'''STRUCTURE OF UP1 PROTEIN'''<br />
 
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==Overview==
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==Structure of UP1 protein==
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The Kae1 (Kinase-associated endopeptidase 1) protein is a member of the, recently identified transcription complex EKC and telomeres maintenance, complex KEOPS in yeast. Kae1 homologues are encoded by all sequenced, genomes in the three domains of life. Although annotated as putative, endopeptidases, the actual functions of these universal proteins are, unknown. Here we show that the purified Kae1 protein (Pa-Kae1) from, Pyrococcus abyssi is an iron-protein with a novel type of ATP-binding, site. Surprisingly, this protein did not exhibit endopeptidase activity in, vitro but binds cooperatively to single and double-stranded DNA and, induces unusual DNA conformational change. Furthermore, Pa-Kae1 exhibits a, class I apurinic (AP)-endonuclease activity (AP-lyase). Both DNA binding, and AP-endonuclease activity are inhibited by ATP. Kae1 is thus a novel, and atypical universal DNA interacting protein whose importance could, rival those of RecA (RadA/Rad51) in the maintenance of genome integrity in, all living cells.
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<StructureSection load='2ivn' size='340' side='right'caption='[[2ivn]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2ivn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IVN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IVN FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ivn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ivn OCA], [https://pdbe.org/2ivn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ivn RCSB], [https://www.ebi.ac.uk/pdbsum/2ivn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ivn ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/KAE1_PYRAB KAE1_PYRAB] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is a component of the KEOPS complex that is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37. Kae1 likely plays a direct catalytic role in this reaction, but requires other protein(s) of the complex to fulfill this activity. In vitro, binds tRNA, ssRNA, both single- and double-stranded DNA, and exhibits a low ATPase activity.[HAMAP-Rule:MF_01446]<ref>PMID:17766251</ref> <ref>PMID:19143597</ref> <ref>PMID:23258706</ref> <ref>PMID:23945934</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/2ivn_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2ivn ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The Kae1 (Kinase-associated endopeptidase 1) protein is a member of the recently identified transcription complex EKC and telomeres maintenance complex KEOPS in yeast. Kae1 homologues are encoded by all sequenced genomes in the three domains of life. Although annotated as putative endopeptidases, the actual functions of these universal proteins are unknown. Here we show that the purified Kae1 protein (Pa-Kae1) from Pyrococcus abyssi is an iron-protein with a novel type of ATP-binding site. Surprisingly, this protein did not exhibit endopeptidase activity in vitro but binds cooperatively to single and double-stranded DNA and induces unusual DNA conformational change. Furthermore, Pa-Kae1 exhibits a class I apurinic (AP)-endonuclease activity (AP-lyase). Both DNA binding and AP-endonuclease activity are inhibited by ATP. Kae1 is thus a novel and atypical universal DNA interacting protein whose importance could rival those of RecA (RadA/Rad51) in the maintenance of genome integrity in all living cells.
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==About this Structure==
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An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro.,Hecker A, Leulliot N, Gadelle D, Graille M, Justome A, Dorlet P, Brochier C, Quevillon-Cheruel S, Le Cam E, van Tilbeurgh H, Forterre P Nucleic Acids Res. 2007;35(18):6042-51. Epub 2007 Aug 30. PMID:17766251<ref>PMID:17766251</ref>
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2IVN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi] with MG, ANP and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/O-sialoglycoprotein_endopeptidase O-sialoglycoprotein endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.57 3.4.24.57] Known structural/functional Sites: <scene name='pdbsite=AC1:Gol Binding Site For Chain A'>AC1</scene>, <scene name='pdbsite=AC2:Anp Binding Site For Chain A'>AC2</scene> and <scene name='pdbsite=AC3:Mg Binding Site For Chain A'>AC3</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2IVN OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro., Hecker A, Leulliot N, Gadelle D, Graille M, Justome A, Dorlet P, Brochier C, Quevillon-Cheruel S, Le Cam E, van Tilbeurgh H, Forterre P, Nucleic Acids Res. 2007;35(18):6042-51. Epub 2007 Aug 30. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17766251 17766251]
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</div>
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[[Category: O-sialoglycoprotein endopeptidase]]
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<div class="pdbe-citations 2ivn" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pyrococcus abyssi]]
[[Category: Pyrococcus abyssi]]
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[[Category: Single protein]]
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[[Category: Dorlet P]]
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[[Category: Dorlet, P.]]
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[[Category: Forterre P]]
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[[Category: Forterre, P.]]
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[[Category: Graille M]]
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[[Category: Graille, M.]]
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[[Category: Hecker A]]
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[[Category: Hecker, A.]]
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[[Category: Leulliot N]]
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[[Category: Leulliot, N.]]
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[[Category: Quevillon-Cheruel S]]
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[[Category: Quevillon-Cheruel, S.]]
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[[Category: Ulryck N]]
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[[Category: Tilbeurgh, H.Van.]]
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[[Category: Van Tilbeurgh H]]
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[[Category: Ulryck, N.]]
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[[Category: ANP]]
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[[Category: GOL]]
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[[Category: MG]]
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[[Category: fe/zn dependent nucleotide phosphatase]]
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[[Category: hydrolase]]
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[[Category: hypothetical protein]]
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[[Category: metal-binding]]
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[[Category: metalloprotease]]
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[[Category: protease]]
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[[Category: up1 keops complex]]
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[[Category: zinc]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 19:36:35 2007''
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Current revision

Structure of UP1 protein

PDB ID 2ivn

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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