3q1r

From Proteopedia

(Difference between revisions)

Revision as of 05:48, 8 June 2022

Crystal structure of a bacterial RNase P holoenzyme in complex with TRNA and in the presence of 5' leader

Structural highlights

3q1r is a 4 chain structure with sequence from Atcc 43589. This structure supersedes the now removed PDB entry 3okb. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	2a2e, 2a64, 1u9s, 1nbs, 1nz0, 1ehz, 3q1q
Gene:	rnpA, RNPA OR TM1463, RNPB, TM_1463 (ATCC 43589)
Activity:	Ribonuclease P, with EC number 3.1.26.5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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).

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^[1]

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

References

↑ Reiter NJ, Osterman A, Torres-Larios A, Swinger KK, Pan T, Mondragon A. Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. Nature. 2010 Nov 14. PMID:21076397 doi:10.1038/nature09516

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3q1r"

@@ Line 1: / Line 1: @@
 ==Crystal structure of a bacterial RNase P holoenzyme in complex with TRNA and in the presence of 5' leader==
-<StructureSection load='3q1r' size='340' side='right' caption='[[3q1r]], [[Resolution|resolution]] 4.21&Aring;' scene=''>
+<StructureSection load='3q1r' size='340' side='right'caption='[[3q1r]], [[Resolution|resolution]] 4.21&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3q1r]] is a 4 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/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/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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2a2e|2a2e]], [[2a64|2a64]], [[1u9s|1u9s]], [[1nbs|1nbs]], [[1nz0|1nz0]], [[1ehz|1ehz]], [[3q1q|3q1q]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rnpA, RNPA OR TM1463, RNPB, TM_1463 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</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'>[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] </span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3q1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q1r OCA], [http://pdbe.org/3q1r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3q1r RCSB], [http://www.ebi.ac.uk/pdbsum/3q1r PDBsum], [http://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>
 == Function ==
-[[http://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 ==
@@ Line 23: / Line 23: @@
 ==See Also==
-*[[Ribonuclease|Ribonuclease]]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-*[[TRNA|TRNA]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-*[[Temp|Temp]]
 == References ==
 <references/>
@@ Line 31: / Line 30: @@
 </StructureSection>
 [[Category: Atcc 43589]]
+[[Category: Large Structures]]
 [[Category: Ribonuclease P]]
 [[Category: Mondragon, A]]

3q1r

From Proteopedia

Revision as of 05:48, 8 June 2022

Crystal structure of a bacterial RNase P holoenzyme in complex with TRNA and in the presence of 5' leader

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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