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| - | [[Image:1x0t.gif|left|200px]]<br /><applet load="1x0t" size="450" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1x0t, resolution 1.60Å" /> | |
| - | '''Crystal structure of ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3'''<br /> | |
| | | | |
| - | ==Overview== | + | ==Crystal structure of ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3== |
| - | Ribonuclease P (RNase P) is a ribonucleoprotein complex involved in the, removal of 5' leader sequences from tRNA precursors (pre-tRNA). The human, protein Rpp21 is essential for human RNase P activity in tRNA processing, in vitro. The crystal structure of Ph1601p from the hyperthermophilic, archaeon Pyrococcus horikoshii OT3, the archaeal homologue of Rpp21, was, determined using the multiple anomalous dispersion (MAD) method with the, aid of anomalous scattering in zinc and selenium at 1.6 A resolution., Ph1601p comprises an N-terminal domain (residues 1-55), a central linker, domain (residues 56-79), and a C-terminal domain (residues 80-120), forming an L-shaped structure. The N-terminal domain consists of two long, alpha-helices, while the central and C-terminal domains fold in a zinc, ribbon domain. The electrostatic potential representation indicates the, presence of positively charged clusters along the L arms, suggesting a, possible role in RNA binding. A single zinc ion binds the well-ordered, binding site that consists of four Cys residues (Cys68, Cys71, Cys97, and, Cys100) and appears to stabilize the relative positions of the N- and, C-domains. Mutations of Cys68 and Cys71 or Cys97 and Cys100 to Ser, destabilize the protein structure, which results in inactivation of the, RNase P activity. In addition, site-directed mutagenesis suggests that, Lys69 at the central loop and Arg86 and Arg105 at the zinc ribbon domain, are strongly involved in the functional activity, while Arg22, Tyr44, Arg65, and Arg84 play a modest role in the activity.
| + | <StructureSection load='1x0t' size='340' side='right'caption='[[1x0t]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[1x0t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X0T 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]] 1.6Å</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1x0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x0t OCA], [https://pdbe.org/1x0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x0t RCSB], [https://www.ebi.ac.uk/pdbsum/1x0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x0t ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/RNP4_PYRHO RNP4_PYRHO] Part of ribonuclease 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:16142906</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/x0/1x0t_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=1x0t ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | ==About this Structure== | + | ==See Also== |
| - | 1X0T 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 ZN 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=1X0T OCA].
| + | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] |
| - | | + | == References == |
| - | ==Reference== | + | <references/> |
| - | Crystal structure of a ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3: an archaeal homologue of human nuclear ribonuclease P protein Rpp21., Kakuta Y, Ishimatsu I, Numata T, Kimura K, Yao M, Tanaka I, Kimura M, Biochemistry. 2005 Sep 13;44(36):12086-93. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16142906 16142906]
| + | __TOC__ |
| - | [[Category: Pyrococcus horikoshii]] | + | </StructureSection> |
| - | [[Category: Ribonuclease P]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]]
| + | [[Category: Pyrococcus horikoshii OT3]] |
| - | [[Category: Ishimatsu, I.]] | + | [[Category: Ishimatsu I]] |
| - | [[Category: Kakuta, Y.]] | + | [[Category: Kakuta Y]] |
| - | [[Category: Kimura, K.]] | + | [[Category: Kimura K]] |
| - | [[Category: Kimura, M.]] | + | [[Category: Kimura M]] |
| - | [[Category: Numata, T.]] | + | [[Category: Numata T]] |
| - | [[Category: Tanaka, I.]] | + | [[Category: Tanaka I]] |
| - | [[Category: Yao, M.]] | + | [[Category: Yao M]] |
| - | [[Category: ZN]]
| + | |
| - | [[Category: pyrococcus horikoshii ot3]]
| + | |
| - | [[Category: ribonuclease p protein]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:46:52 2007''
| + | |
| Structural highlights
Function
RNP4_PYRHO Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Binds RNase P RNA.[1] [2] [3] [4] [5]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
See Also
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
- ↑ Kakuta Y, Ishimatsu I, Numata T, Kimura K, Yao M, Tanaka I, Kimura M. Crystal structure of a ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3: an archaeal homologue of human nuclear ribonuclease P protein Rpp21. Biochemistry. 2005 Sep 13;44(36):12086-93. PMID:16142906 doi:10.1021/bi050738z
- ↑ 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
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