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[[Image:2czv.gif|left|200px]]


{{Structure
==Crystal structure of archeal RNase P protein ph1481p in complex with ph1877p==
|PDB= 2czv |SIZE=350|CAPTION= <scene name='initialview01'>2czv</scene>, resolution 2.00&Aring;
<StructureSection load='2czv' size='340' side='right'caption='[[2czv]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene> and <scene name='pdbligand=ACY:ACETIC ACID'>ACY</scene>
<table><tr><td colspan='2'>[[2czv]] is a 4 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=2CZV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CZV FirstGlance]. <br>
|ACTIVITY= [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]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
|GENE= PH1877 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii]), PH1481 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</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=2czv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2czv OCA], [https://pdbe.org/2czv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2czv RCSB], [https://www.ebi.ac.uk/pdbsum/2czv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2czv ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RNP3_PYRHO RNP3_PYRHO] Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Not absolutely essential for activity in vitro, however it strongly stimulates activity. Binds RNase P RNA.<ref>PMID:12810070</ref> <ref>PMID:16574071</ref> <ref>PMID:16829535</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/cz/2czv_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=2czv ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ribonuclease P (RNase P) in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of a catalytic RNA and five protein subunits. We previously determined crystal structures of four protein subunits. Ph1481p, an archaeal homologue for human hPop5, is the protein component of the P.horikoshii RNase P for which no structural information is available. Here we report the crystal structure of Ph1481p in complex with another protein subunit, Ph1877p, determined at 2.0 A resolution. Ph1481p consists of a five-stranded antiparallel beta-sheet and five helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. Ph1481p is, however, distinct from the typical RNP domain in that it has additional helices at the C terminus, which pack against one face of the beta-sheet. The presence of two complexes in the asymmetric unit, together with gel filtration chromatography indicates that the heterotetramer is stable in solution and represents a fundamental building block in the crystals. In the heterotetrameric structure (Ph1877p-(Ph1481p)(2)-Ph1877p), a homodimer of Ph1481p sits between two Ph1877p monomers. Ph1481p dimerizes through hydrogen bonding interaction from the loop between alpha1 and alpha2 helices, and each Ph1481p interacts with two Ph1877p molecules, where alpha2 and alpha3 in Ph1481p interact with alpha7 in one Ph1877p and alpha8 in the other Ph1877p molecule, respectively. Deletion of the alpha1-alpha2 loop in Ph1481p caused heterodimerization with Ph1877p, and abolished ability to homodimerize itself and heterotetramerize with Ph1877p. Furthermore, the reconstituted particle containing the deletion mutant Ph1481p (mPh1481p) exhibited significantly reduced nuclease activity. These results suggest the presence of the heterotetramer of Ph1481p and Ph1877p in P.horikoshii RNase P.


'''Crystal structure of archeal RNase P protein ph1481p in complex with ph1877p'''
Crystal structure of protein Ph1481p in complex with protein Ph1877p of archaeal RNase P from Pyrococcus horikoshii OT3: implication of dimer formation of the holoenzyme.,Kawano S, Nakashima T, Kakuta Y, Tanaka I, Kimura M J Mol Biol. 2006 Mar 24;357(2):583-91. Epub 2006 Jan 11. PMID:16430919<ref>PMID:16430919</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2czv" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
Ribonuclease P (RNase P) in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of a catalytic RNA and five protein subunits. We previously determined crystal structures of four protein subunits. Ph1481p, an archaeal homologue for human hPop5, is the protein component of the P.horikoshii RNase P for which no structural information is available. Here we report the crystal structure of Ph1481p in complex with another protein subunit, Ph1877p, determined at 2.0 A resolution. Ph1481p consists of a five-stranded antiparallel beta-sheet and five helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. Ph1481p is, however, distinct from the typical RNP domain in that it has additional helices at the C terminus, which pack against one face of the beta-sheet. The presence of two complexes in the asymmetric unit, together with gel filtration chromatography indicates that the heterotetramer is stable in solution and represents a fundamental building block in the crystals. In the heterotetrameric structure (Ph1877p-(Ph1481p)(2)-Ph1877p), a homodimer of Ph1481p sits between two Ph1877p monomers. Ph1481p dimerizes through hydrogen bonding interaction from the loop between alpha1 and alpha2 helices, and each Ph1481p interacts with two Ph1877p molecules, where alpha2 and alpha3 in Ph1481p interact with alpha7 in one Ph1877p and alpha8 in the other Ph1877p molecule, respectively. Deletion of the alpha1-alpha2 loop in Ph1481p caused heterodimerization with Ph1877p, and abolished ability to homodimerize itself and heterotetramerize with Ph1877p. Furthermore, the reconstituted particle containing the deletion mutant Ph1481p (mPh1481p) exhibited significantly reduced nuclease activity. These results suggest the presence of the heterotetramer of Ph1481p and Ph1877p in P.horikoshii RNase P.
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
 
== References ==
==About this Structure==
<references/>
2CZV is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZV OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
Crystal structure of protein Ph1481p in complex with protein Ph1877p of archaeal RNase P from Pyrococcus horikoshii OT3: implication of dimer formation of the holoenzyme., Kawano S, Nakashima T, Kakuta Y, Tanaka I, Kimura M, J Mol Biol. 2006 Mar 24;357(2):583-91. Epub 2006 Jan 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16430919 16430919]
[[Category: Protein complex]]
[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii]]
[[Category: Ribonuclease P]]
[[Category: Kakuta Y]]
[[Category: Kakuta, Y.]]
[[Category: Kawano S]]
[[Category: Kawano, S.]]
[[Category: Kimura M]]
[[Category: Kimura, M.]]
[[Category: Nakashima T]]
[[Category: Nakashima, T.]]
[[Category: Tanaka I]]
[[Category: Tanaka, I.]]
[[Category: ACY]]
[[Category: BOG]]
[[Category: protein-protein complex]]
[[Category: ribonuclease]]
[[Category: rna binding protein]]
[[Category: rna recognition motif]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:21:39 2008''

Latest revision as of 14:32, 22 May 2024

Crystal structure of archeal RNase P protein ph1481p in complex with ph1877pCrystal structure of archeal RNase P protein ph1481p in complex with ph1877p

Structural highlights

2czv is a 4 chain structure with sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNP3_PYRHO Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Not absolutely essential for activity in vitro, however it strongly stimulates activity. Binds RNase P RNA.[1] [2] [3]

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) in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of a catalytic RNA and five protein subunits. We previously determined crystal structures of four protein subunits. Ph1481p, an archaeal homologue for human hPop5, is the protein component of the P.horikoshii RNase P for which no structural information is available. Here we report the crystal structure of Ph1481p in complex with another protein subunit, Ph1877p, determined at 2.0 A resolution. Ph1481p consists of a five-stranded antiparallel beta-sheet and five helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. Ph1481p is, however, distinct from the typical RNP domain in that it has additional helices at the C terminus, which pack against one face of the beta-sheet. The presence of two complexes in the asymmetric unit, together with gel filtration chromatography indicates that the heterotetramer is stable in solution and represents a fundamental building block in the crystals. In the heterotetrameric structure (Ph1877p-(Ph1481p)(2)-Ph1877p), a homodimer of Ph1481p sits between two Ph1877p monomers. Ph1481p dimerizes through hydrogen bonding interaction from the loop between alpha1 and alpha2 helices, and each Ph1481p interacts with two Ph1877p molecules, where alpha2 and alpha3 in Ph1481p interact with alpha7 in one Ph1877p and alpha8 in the other Ph1877p molecule, respectively. Deletion of the alpha1-alpha2 loop in Ph1481p caused heterodimerization with Ph1877p, and abolished ability to homodimerize itself and heterotetramerize with Ph1877p. Furthermore, the reconstituted particle containing the deletion mutant Ph1481p (mPh1481p) exhibited significantly reduced nuclease activity. These results suggest the presence of the heterotetramer of Ph1481p and Ph1877p in P.horikoshii RNase P.

Crystal structure of protein Ph1481p in complex with protein Ph1877p of archaeal RNase P from Pyrococcus horikoshii OT3: implication of dimer formation of the holoenzyme.,Kawano S, Nakashima T, Kakuta Y, Tanaka I, Kimura M J Mol Biol. 2006 Mar 24;357(2):583-91. Epub 2006 Jan 11. PMID:16430919[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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. ↑ Kawano S, Nakashima T, Kakuta Y, Tanaka I, Kimura M. Crystal structure of protein Ph1481p in complex with protein Ph1877p of archaeal RNase P from Pyrococcus horikoshii OT3: implication of dimer formation of the holoenzyme. J Mol Biol. 2006 Mar 24;357(2):583-91. Epub 2006 Jan 11. PMID:16430919 doi:10.1016/j.jmb.2005.12.086

2czv, resolution 2.00Å

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