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| - | ==STRUCTURE OF UP1 PROTEIN== | + | |
| - | <StructureSection load='2ivn' size='340' side='right' caption='[[2ivn]], [[Resolution|resolution]] 1.65Å' scene=''> | + | ==Structure of UP1 protein== |
| | + | <StructureSection load='2ivn' size='340' side='right'caption='[[2ivn]], [[Resolution|resolution]] 1.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2ivn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IVN FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ivo|2ivo]], [[2ivp|2ivp]]</td></tr> | + | <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> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=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> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ivn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ivn OCA], [http://pdbe.org/2ivn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ivn RCSB], [http://www.ebi.ac.uk/pdbsum/2ivn PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/2ivn_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/2ivn_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </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/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </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]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pyrococcus abyssi erauso et al. 1993]] | + | [[Category: Large Structures]] |
| - | [[Category: O-sialoglycoprotein endopeptidase]] | + | [[Category: Pyrococcus abyssi]] |
| - | [[Category: Dorlet, P]] | + | [[Category: Dorlet P]] |
| - | [[Category: Forterre, P]] | + | [[Category: Forterre P]] |
| - | [[Category: Graille, M]] | + | [[Category: Graille M]] |
| - | [[Category: Hecker, A]] | + | [[Category: Hecker A]] |
| - | [[Category: Leulliot, N]] | + | [[Category: Leulliot N]] |
| - | [[Category: Quevillon-Cheruel, S]] | + | [[Category: Quevillon-Cheruel S]] |
| - | [[Category: Tilbeurgh, H Van]]
| + | [[Category: Ulryck N]] |
| - | [[Category: Ulryck, N]] | + | [[Category: Van Tilbeurgh H]] |
| - | [[Category: Fe/zn dependent nucleotide phosphatase]] | + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Hypothetical protein]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Metalloprotease]]
| + | |
| - | [[Category: Protease]]
| + | |
| - | [[Category: Up1 keops complex]]
| + | |
| Structural highlights
Function
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][1] [2] [3] [4]
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 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.
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[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ 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. An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro. Nucleic Acids Res. 2007;35(18):6042-51. Epub 2007 Aug 30. PMID:17766251 doi:10.1093/nar/gkm554
- ↑ Hecker A, Graille M, Madec E, Gadelle D, Le Cam E, van Tilbergh H, Forterre P. The universal Kae1 protein and the associated Bud32 kinase (PRPK), a mysterious protein couple probably essential for genome maintenance in Archaea and Eukarya. Biochem Soc Trans. 2009 Feb;37(Pt 1):29-35. doi: 10.1042/BST0370029. PMID:19143597 doi:http://dx.doi.org/10.1042/BST0370029
- ↑ Perrochia L, Crozat E, Hecker A, Zhang W, Bareille J, Collinet B, van Tilbeurgh H, Forterre P, Basta T. In vitro biosynthesis of a universal t6A tRNA modification in Archaea and Eukarya. Nucleic Acids Res. 2013 Feb 1;41(3):1953-64. doi: 10.1093/nar/gks1287. Epub 2012 , Dec 20. PMID:23258706 doi:http://dx.doi.org/10.1093/nar/gks1287
- ↑ Perrochia L, Guetta D, Hecker A, Forterre P, Basta T. Functional assignment of KEOPS/EKC complex subunits in the biosynthesis of the universal t6A tRNA modification. Nucleic Acids Res. 2013 Nov;41(20):9484-99. doi: 10.1093/nar/gkt720. Epub 2013, Aug 14. PMID:23945934 doi:http://dx.doi.org/10.1093/nar/gkt720
- ↑ 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. An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro. Nucleic Acids Res. 2007;35(18):6042-51. Epub 2007 Aug 30. PMID:17766251 doi:10.1093/nar/gkm554
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