3q1q

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<StructureSection load='3q1q' size='340' side='right'caption='[[3q1q]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
<StructureSection load='3q1q' size='340' side='right'caption='[[3q1q]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3q1q]] is a 3 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=3ok7 3ok7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q1Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q1Q FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3q1q]] is a 3 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=3ok7 3ok7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q1Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q1Q FirstGlance]. <br>
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</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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.8&#8491;</td></tr>
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<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]], [[3q1r|3q1r]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<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>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3q1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q1q OCA], [https://pdbe.org/3q1q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q1q RCSB], [https://www.ebi.ac.uk/pdbsum/3q1q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q1q 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=3q1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q1q OCA], [https://pdbe.org/3q1q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q1q RCSB], [https://www.ebi.ac.uk/pdbsum/3q1q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q1q ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[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).
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[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).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3q1q" style="background-color:#fffaf0;"></div>
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==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)]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Atcc 43589]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Ribonuclease P]]
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[[Category: Thermotoga maritima]]
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[[Category: Mondragon, A]]
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[[Category: Mondragon A]]
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[[Category: Osterman, A]]
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[[Category: Osterman A]]
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[[Category: Pan, T]]
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[[Category: Pan T]]
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[[Category: Reiter, N J]]
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[[Category: Reiter NJ]]
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[[Category: Swinger, K K]]
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[[Category: Swinger KK]]
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[[Category: Torres-Larios, A]]
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[[Category: Torres-Larios A]]
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[[Category: A-minor interaction]]
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[[Category: Base stacking]]
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[[Category: Endonuclease]]
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[[Category: Enzyme-product complex]]
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[[Category: Hydrolase-rna complex]]
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[[Category: Intermolecular base pair]]
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[[Category: Intermolecular rna-rna contact]]
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[[Category: Metalloenzyme]]
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[[Category: Pre-trna]]
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[[Category: Ribonuclease p]]
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[[Category: Ribonucleoprotein complex]]
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[[Category: Ribose zipper]]
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[[Category: Ribozyme]]
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[[Category: Rna-metal interaction]]
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[[Category: Rnase p]]
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[[Category: Rnp]]
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[[Category: Shape complementarity]]
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[[Category: Tetraloop-receptor]]
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[[Category: Trna]]
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Current revision

Structure of a Bacterial Ribonuclease P Holoenzyme in Complex with tRNA

PDB ID 3q1q

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