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| | ==Crystal structure of PhoRpp38-SL12M complex== | | ==Crystal structure of PhoRpp38-SL12M complex== |
| - | <StructureSection load='5dcv' size='340' side='right' caption='[[5dcv]], [[Resolution|resolution]] 3.40Å' scene=''> | + | <StructureSection load='5dcv' size='340' side='right'caption='[[5dcv]], [[Resolution|resolution]] 3.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5dcv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DCV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DCV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5dcv]] is a 4 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=5DCV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DCV FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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]] 3.401Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2czw|2czw]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></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=5dcv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dcv OCA], [http://pdbe.org/5dcv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dcv RCSB], [http://www.ebi.ac.uk/pdbsum/5dcv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dcv 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=5dcv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dcv OCA], [https://pdbe.org/5dcv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dcv RCSB], [https://www.ebi.ac.uk/pdbsum/5dcv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dcv ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RL7A_PYRHO RL7A_PYRHO]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity). When added to reconstituted ribonuclease P (RNase P) it increases the optimum temperature to that of the partially purified enzyme and causes a 5-fold increase in apparent Vmax. Binds the RNase P catalytic RNA.<ref>PMID:16829535</ref> <ref>PMID:16574071</ref> | + | [https://www.uniprot.org/uniprot/RL7A_PYRHO RL7A_PYRHO] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity). When added to reconstituted ribonuclease P (RNase P) it increases the optimum temperature to that of the partially purified enzyme and causes a 5-fold increase in apparent Vmax. Binds the RNase P catalytic RNA.<ref>PMID:16829535</ref> <ref>PMID:16574071</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Oshima, K]] | + | [[Category: Large Structures]] |
| - | [[Category: Tanaka, Y]] | + | [[Category: Pyrococcus horikoshii OT3]] |
| - | [[Category: Yao, M]] | + | [[Category: Oshima K]] |
| - | [[Category: Rna]] | + | [[Category: Tanaka Y]] |
| - | [[Category: Rna binding protein-rna complex]] | + | [[Category: Yao M]] |
| Structural highlights
Function
RL7A_PYRHO Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity). When added to reconstituted ribonuclease P (RNase P) it increases the optimum temperature to that of the partially purified enzyme and causes a 5-fold increase in apparent Vmax. Binds the RNase P catalytic RNA.[1] [2]
Publication Abstract from PubMed
PhoRpp38 in the hyperthermophilic archaeon Pyrococcus horikoshii, a homologue of human ribonuclease P (RNase P) protein Rpp38, belongs to the ribosomal protein L7Ae family that specifically recognizes a kink-turn (K-turn) motif. A previous biochemical study showed that PhoRpp38 specifically binds to two stem-loops, SL12 and SL16, containing helices P12.1/12.2 and P15/16 respectively, in P. horikoshii RNase P RNA (PhopRNA). In order to gain insight into the PhoRpp38 binding mode to PhopRNA, we determined the crystal structure of PhoRpp38 in complex with the SL12 mutant (SL12M) at a resolution of 3.4 A. The structure revealed that Lys35 on the beta-strand (beta1) and Asn38, Glu39, and Lys42 on the alpha-helix (alpha2) in PhoRpp38 interact with characteristic G*A and A*G pairs in SL12M, where Ile93, Glu94, and Val95, on a loop between alpha4 and beta4 in PhoRpp38, interact with the 3-nucleotide bulge (G-G-U) in the SL12M. The structure demonstrates the previously proposed secondary structure of SL12, including helix P12.2. Structure-based mutational analysis indicated that amino acid residues involved in the binding to SL12 are also responsible for the binding to SL16. This result suggested that each PhoRpp38 binds to the K-turns in SL12 and SL16 in PhopRNA. A pull-down assay further suggested the presence of a second K-turn in SL12. Based on the present results, together with available data, we discuss a structural basis for recognition of K-turn motifs in PhopRNA by PhoRpp38.
Structural basis for recognition of a kink-turn motif by an archaeal homologue of human RNase P protein Rpp38.,Oshima K, Kakiuchi Y, Tanaka Y, Ueda T, Nakashima T, Kimura M, Yao M Biochem Biophys Res Commun. 2016 Jun 3;474(3):541-6. doi:, 10.1016/j.bbrc.2016.04.118. Epub 2016 Apr 23. PMID:27114305[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ 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
- ↑ 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
- ↑ Oshima K, Kakiuchi Y, Tanaka Y, Ueda T, Nakashima T, Kimura M, Yao M. Structural basis for recognition of a kink-turn motif by an archaeal homologue of human RNase P protein Rpp38. Biochem Biophys Res Commun. 2016 Jun 3;474(3):541-6. doi:, 10.1016/j.bbrc.2016.04.118. Epub 2016 Apr 23. PMID:27114305 doi:http://dx.doi.org/10.1016/j.bbrc.2016.04.118
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