|
|
| Line 3: |
Line 3: |
| <StructureSection load='3q1r' size='340' side='right'caption='[[3q1r]], [[Resolution|resolution]] 4.21Å' scene=''> | | <StructureSection load='3q1r' size='340' side='right'caption='[[3q1r]], [[Resolution|resolution]] 4.21Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[3q1r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3okb 3okb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q1R FirstGlance]. <br> | | <table><tr><td colspan='2'>[[3q1r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3okb 3okb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q1R FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 4.21Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2a2e|2a2e]], [[2a64|2a64]], [[1u9s|1u9s]], [[1nbs|1nbs]], [[1nz0|1nz0]], [[1ehz|1ehz]], [[3q1q|3q1q]]</div></td></tr>
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rnpA, RNPA OR TM1463, RNPB, TM_1463 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3q1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q1r OCA], [https://pdbe.org/3q1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q1r RCSB], [https://www.ebi.ac.uk/pdbsum/3q1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q1r 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=3q1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q1r OCA], [https://pdbe.org/3q1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q1r RCSB], [https://www.ebi.ac.uk/pdbsum/3q1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q1r ProSAT]</span></td></tr> |
| </table> | | </table> |
| == Function == | | == Function == |
| [[https://www.uniprot.org/uniprot/RNPA_THEMA RNPA_THEMA]] RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme (By similarity).
| | [https://www.uniprot.org/uniprot/RNPA_THEMA RNPA_THEMA] RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme (By similarity). |
| <div style="background-color:#fffaf0;">
| |
| == Publication Abstract from PubMed ==
| |
| Ribonuclease (RNase) P is the universal ribozyme responsible for 5'-end tRNA processing. We report the crystal structure of the Thermotoga maritima RNase P holoenzyme in complex with tRNA(Phe). The 154 kDa complex consists of a large catalytic RNA (P RNA), a small protein cofactor and a mature tRNA. The structure shows that RNA-RNA recognition occurs through shape complementarity, specific intermolecular contacts and base-pairing interactions. Soaks with a pre-tRNA 5' leader sequence with and without metal help to identify the 5' substrate path and potential catalytic metal ions. The protein binds on top of a universally conserved structural module in P RNA and interacts with the leader, but not with the mature tRNA. The active site is composed of phosphate backbone moieties, a universally conserved uridine nucleobase, and at least two catalytically important metal ions. The active site structure and conserved RNase P-tRNA contacts suggest a universal mechanism of catalysis by RNase P.
| |
| | |
| Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA.,Reiter NJ, Osterman A, Torres-Larios A, Swinger KK, Pan T, Mondragon A Nature. 2010 Nov 14. PMID:21076397<ref>PMID:21076397</ref>
| |
| | |
| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| |
| </div>
| |
| <div class="pdbe-citations 3q1r" style="background-color:#fffaf0;"></div>
| |
|
| |
|
| ==See Also== | | ==See Also== |
| *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] |
| *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] |
| == References ==
| |
| <references/>
| |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Atcc 43589]]
| |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: Ribonuclease P]] | | [[Category: Thermotoga maritima]] |
| [[Category: Mondragon, A]] | | [[Category: Mondragon A]] |
| [[Category: Ostermanm, A]] | | [[Category: Ostermanm A]] |
| [[Category: Pan, T]] | | [[Category: Pan T]] |
| [[Category: Reiter, N J]] | | [[Category: Reiter NJ]] |
| [[Category: Swinger, K K]] | | [[Category: Swinger KK]] |
| [[Category: Torres-Larios, A]] | | [[Category: Torres-Larios A]] |
| [[Category: A-minor interaction]]
| |
| [[Category: Base stacking]]
| |
| [[Category: Endonuclease]]
| |
| [[Category: Enzyme-product complex]]
| |
| [[Category: Hydrolase-rna complex]]
| |
| [[Category: Intermolecular base pair]]
| |
| [[Category: Intermolecular rna-rna contact]]
| |
| [[Category: Metalloenzyme]]
| |
| [[Category: Pre-trna]]
| |
| [[Category: Ribonuclease p]]
| |
| [[Category: Ribonucleoprotein complex]]
| |
| [[Category: Ribose zipper]]
| |
| [[Category: Ribozyme]]
| |
| [[Category: Rna-metal interaction]]
| |
| [[Category: Rnase p]]
| |
| [[Category: Rnp]]
| |
| [[Category: Shape complementarity]]
| |
| [[Category: Substrate recognition]]
| |
| [[Category: Tetraloop-receptor]]
| |
| [[Category: Trna]]
| |