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| - | [[Image:1v76.gif|left|200px]]<br /><applet load="1v76" size="450" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1v76, resolution 2.00Å" /> | |
| - | '''Crystal Structure of Archaeal Ribonuclease P Protein Ph1771p from Pyrococcus horikoshii OT3'''<br /> | |
| | | | |
| - | ==Overview== | + | ==Crystal Structure of Archaeal Ribonuclease P Protein Ph1771p from Pyrococcus horikoshii OT3== |
| - | Ribonuclease P (RNase P) is the endonuclease responsible for the removal, of 5' leader sequences from tRNA precursors. The crystal structure of an, archaeal RNase P protein, Ph1771p (residues 36-127) from hyperthermophilic, archaeon Pyrococcus horikoshii OT3 was determined at 2.0 A resolution by, X-ray crystallography. The structure is composed of four helices, (alpha1-alpha4) and a six-stranded antiparallel beta-sheet (beta1-beta6), with a protruding beta-strand (beta7) at the C-terminal region. The strand, beta7 forms an antiparallel beta-sheet by interacting with strand beta4 in, a symmetry-related molecule, suggesting that strands beta4 and beta7 could, be involved in protein-protein interactions with other RNase P proteins., Structural comparison showed that the beta-barrel structure of Ph1771p has, a topological resemblance to those of Staphylococcus aureus translational, regulator Hfq and Haloarcula marismortui ribosomal protein L21E, suggesting that these RNA binding proteins have a common ancestor and then, diverged to specifically bind to their cognate RNAs. The structure, analysis as well as structural comparison suggested two possible RNA, binding sites in Ph1771p, one being a concave surface formed by terminal, alpha-helices (alpha1-alpha4) and beta-strand beta6, where positively, charged residues are clustered. A second possible RNA binding site is at a, loop region connecting strands beta2 and beta3, where conserved, hydrophilic residues are exposed to the solvent and interact specifically, with sulfate ion. These two potential sites for RNA binding are located in, close proximity. The crystal structure of Ph1771p provides insight into, the structure and function relationships of archaeal and eukaryotic RNase, P. | + | <StructureSection load='1v76' size='340' side='right'caption='[[1v76]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[1v76]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V76 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V76 FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1v76 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v76 OCA], [https://pdbe.org/1v76 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v76 RCSB], [https://www.ebi.ac.uk/pdbsum/1v76 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v76 ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/RNP1_PYRHO RNP1_PYRHO] Part of ribonuclease P (RNase P), a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Binds RNase P RNA.<ref>PMID:12810070</ref> <ref>PMID:16574071</ref> <ref>PMID:16829535</ref> <ref>PMID:18929577</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/v7/1v76_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=1v76 ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Ribonuclease P (RNase P) is the endonuclease responsible for the removal of 5' leader sequences from tRNA precursors. The crystal structure of an archaeal RNase P protein, Ph1771p (residues 36-127) from hyperthermophilic archaeon Pyrococcus horikoshii OT3 was determined at 2.0 A resolution by X-ray crystallography. The structure is composed of four helices (alpha1-alpha4) and a six-stranded antiparallel beta-sheet (beta1-beta6) with a protruding beta-strand (beta7) at the C-terminal region. The strand beta7 forms an antiparallel beta-sheet by interacting with strand beta4 in a symmetry-related molecule, suggesting that strands beta4 and beta7 could be involved in protein-protein interactions with other RNase P proteins. Structural comparison showed that the beta-barrel structure of Ph1771p has a topological resemblance to those of Staphylococcus aureus translational regulator Hfq and Haloarcula marismortui ribosomal protein L21E, suggesting that these RNA binding proteins have a common ancestor and then diverged to specifically bind to their cognate RNAs. The structure analysis as well as structural comparison suggested two possible RNA binding sites in Ph1771p, one being a concave surface formed by terminal alpha-helices (alpha1-alpha4) and beta-strand beta6, where positively charged residues are clustered. A second possible RNA binding site is at a loop region connecting strands beta2 and beta3, where conserved hydrophilic residues are exposed to the solvent and interact specifically with sulfate ion. These two potential sites for RNA binding are located in close proximity. The crystal structure of Ph1771p provides insight into the structure and function relationships of archaeal and eukaryotic RNase P. |
| | | | |
| - | ==About this Structure==
| + | Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29.,Numata T, Ishimatsu I, Kakuta Y, Tanaka I, Kimura M RNA. 2004 Sep;10(9):1423-32. PMID:15317976<ref>PMID:15317976</ref> |
| - | 1V76 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1V76 OCA].
| + | |
| | | | |
| - | ==Reference==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29., Numata T, Ishimatsu I, Kakuta Y, Tanaka I, Kimura M, RNA. 2004 Sep;10(9):1423-32. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15317976 15317976]
| + | </div> |
| | + | <div class="pdbe-citations 1v76" style="background-color:#fffaf0;"></div> |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Pyrococcus horikoshii]] | | [[Category: Pyrococcus horikoshii]] |
| - | [[Category: Ribonuclease P]]
| + | [[Category: Kakuta Y]] |
| - | [[Category: Single protein]]
| + | [[Category: Kimura M]] |
| - | [[Category: Kakuta, Y.]] | + | [[Category: Numata T]] |
| - | [[Category: Kimura, M.]] | + | |
| - | [[Category: Numata, T.]] | + | |
| - | [[Category: SO4]]
| + | |
| - | [[Category: archaeal rnase p protein]]
| + | |
| - | [[Category: rna binding protein]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 04:29:22 2007''
| + | |
| Structural highlights
Function
RNP1_PYRHO Part of ribonuclease P (RNase P), a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Binds RNase P RNA.[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
Ribonuclease P (RNase P) is the endonuclease responsible for the removal of 5' leader sequences from tRNA precursors. The crystal structure of an archaeal RNase P protein, Ph1771p (residues 36-127) from hyperthermophilic archaeon Pyrococcus horikoshii OT3 was determined at 2.0 A resolution by X-ray crystallography. The structure is composed of four helices (alpha1-alpha4) and a six-stranded antiparallel beta-sheet (beta1-beta6) with a protruding beta-strand (beta7) at the C-terminal region. The strand beta7 forms an antiparallel beta-sheet by interacting with strand beta4 in a symmetry-related molecule, suggesting that strands beta4 and beta7 could be involved in protein-protein interactions with other RNase P proteins. Structural comparison showed that the beta-barrel structure of Ph1771p has a topological resemblance to those of Staphylococcus aureus translational regulator Hfq and Haloarcula marismortui ribosomal protein L21E, suggesting that these RNA binding proteins have a common ancestor and then diverged to specifically bind to their cognate RNAs. The structure analysis as well as structural comparison suggested two possible RNA binding sites in Ph1771p, one being a concave surface formed by terminal alpha-helices (alpha1-alpha4) and beta-strand beta6, where positively charged residues are clustered. A second possible RNA binding site is at a loop region connecting strands beta2 and beta3, where conserved hydrophilic residues are exposed to the solvent and interact specifically with sulfate ion. These two potential sites for RNA binding are located in close proximity. The crystal structure of Ph1771p provides insight into the structure and function relationships of archaeal and eukaryotic RNase P.
Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29.,Numata T, Ishimatsu I, Kakuta Y, Tanaka I, Kimura M RNA. 2004 Sep;10(9):1423-32. PMID:15317976[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kouzuma Y, Mizoguchi M, Takagi H, Fukuhara H, Tsukamoto M, Numata T, Kimura M. Reconstitution of archaeal ribonuclease P from RNA and four protein components. Biochem Biophys Res Commun. 2003 Jul 4;306(3):666-73. PMID:12810070
- ↑ Fukuhara H, Kifusa M, Watanabe M, Terada A, Honda T, Numata T, Kakuta Y, Kimura M. A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3. Biochem Biophys Res Commun. 2006 May 12;343(3):956-64. Epub 2006 Mar 15. PMID:16574071 doi:10.1016/j.bbrc.2006.02.192
- ↑ Terada A, Honda T, Fukuhara H, Hada K, Kimura M. Characterization of the archaeal ribonuclease P proteins from Pyrococcus horikoshii OT3. J Biochem. 2006 Aug;140(2):293-8. Epub 2006 Jul 7. PMID:16829535 doi:http://dx.doi.org/10.1093/jb/mvj144
- ↑ Honda T, Kakuta Y, Kimura K, Saho J, Kimura M. Structure of an archaeal homolog of the human protein complex Rpp21-Rpp29 that is a key core component for the assembly of active ribonuclease P. J Mol Biol. 2008 Dec 19;384(3):652-62. Epub 2008 Oct 2. PMID:18929577 doi:S0022-2836(08)01192-3
- ↑ Numata T, Ishimatsu I, Kakuta Y, Tanaka I, Kimura M. Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29. RNA. 2004 Sep;10(9):1423-32. PMID:15317976 doi:10.1261/rna.7560904
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