1x0t: Difference between revisions

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<StructureSection load='1x0t' size='340' side='right'caption='[[1x0t]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
<StructureSection load='1x0t' size='340' side='right'caption='[[1x0t]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1x0t]] is a 1 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=1X0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X0T FirstGlance]. <br>
<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.6&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_P Ribonuclease P], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.5 3.1.26.5] </span></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>
<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>
</table>
== Function ==
== 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>
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1x0t 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=1x0t ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:16142906<ref>PMID:16142906</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1x0t" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii OT3]]
[[Category: Ribonuclease P]]
[[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: Hydrolase]]
[[Category: Pyrococcus horikoshii ot3]]
[[Category: Ribonuclease p protein]]

Latest revision as of 16:35, 13 March 2024

Crystal structure of ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3Crystal structure of ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3

Structural highlights

1x0t is a 1 chain structure with sequence from Pyrococcus horikoshii OT3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ 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
  5. ↑ 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

1x0t, resolution 1.60Å

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