4x4t: Difference between revisions

Revision as of 21:12, 12 April 2023

Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in CCACCA

Structural highlights

4x4t is a 9 chain structure with sequence from Archaeoglobus fulgidus DSM 4304 and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	5BU, GOL, PEG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CCA_ARCFU Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate.^[1]

Publication Abstract from PubMed

Transcription in eukaryotes produces a number of long noncoding RNAs (lncRNAs). Two of these, MALAT1 and Menbeta, generate a tRNA-like small RNA in addition to the mature lncRNA. The stability of these tRNA-like small RNAs and bona fide tRNAs is monitored by the CCA-adding enzyme. Whereas CCA is added to stable tRNAs and tRNA-like transcripts, a second CCA repeat is added to certain unstable transcripts to initiate their degradation. Here, we characterize how these two scenarios are distinguished. Following the first CCA addition cycle, nucleotide binding to the active site triggers a clockwise screw motion, producing torque on the RNA. This ejects stable RNAs, whereas unstable RNAs are refolded while bound to the enzyme and subjected to a second CCA catalytic cycle. Intriguingly, with the CCA-adding enzyme acting as a molecular vise, the RNAs proofread themselves through differential responses to its interrogation between stable and unstable substrates.

On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme.,Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L Cell. 2015 Feb 12;160(4):644-58. doi: 10.1016/j.cell.2015.01.005. Epub 2015 Jan, 29. PMID:25640237^[2]

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

References

↑ Okabe M, Tomita K, Ishitani R, Ishii R, Takeuchi N, Arisaka F, Nureki O, Yokoyama S. Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure. EMBO J. 2003 Nov 3;22(21):5918-27. PMID:14592988 doi:https://dx.doi.org/10.1093/emboj/cdg563
↑ Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L. On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme. Cell. 2015 Feb 12;160(4):644-58. doi: 10.1016/j.cell.2015.01.005. Epub 2015 Jan, 29. PMID:25640237 doi:https://dx.doi.org/10.1016/j.cell.2015.01.005

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Okabe M, Tomita K, Ishitani R, Ishii R, Takeuchi N, Arisaka F, Nureki O, Yokoyama S. Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure. EMBO J. 2003 Nov 3;22(21):5918-27. PMID:14592988 doi:https://dx.doi.org/10.1093/emboj/cdg563

[2] Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L. On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme. Cell. 2015 Feb 12;160(4):644-58. doi: 10.1016/j.cell.2015.01.005. Epub 2015 Jan, 29. PMID:25640237 doi:https://dx.doi.org/10.1016/j.cell.2015.01.005

[1]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='4x4t' size='340' side='right'caption='[[4x4t]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4x4t]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfu Arcfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X4T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4x4t]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus_DSM_4304 Archaeoglobus fulgidus DSM 4304] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X4T FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</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=4x4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x4t OCA], [https://pdbe.org/4x4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x4t RCSB], [https://www.ebi.ac.uk/pdbsum/4x4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x4t ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cca, AF_2156 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/CCA_tRNA_nucleotidyltransferase CCA tRNA nucleotidyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.72 2.7.7.72] </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=4x4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x4t OCA], [http://pdbe.org/4x4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x4t RCSB], [http://www.ebi.ac.uk/pdbsum/4x4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x4t ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CCA_ARCFU CCA_ARCFU]] Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate.<ref>PMID:14592988</ref>
+[https://www.uniprot.org/uniprot/CCA_ARCFU CCA_ARCFU] Catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template. Adds these three nucleotides in the order of C, C, and A to the tRNA nucleotide-73, using CTP and ATP as substrates and producing inorganic pyrophosphate.<ref>PMID:14592988</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 29: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Arcfu]]
+[[Category: Archaeoglobus fulgidus DSM 4304]]
-[[Category: CCA tRNA nucleotidyltransferase]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Joshua-Tor, L]]
+[[Category: Joshua-Tor L]]
-[[Category: Kuhn, C D]]
+[[Category: Kuhn C-D]]
-[[Category: Cca-adding enzyme]]
-[[Category: Ncrna]]
-[[Category: Non-coding rna]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Protein-rna complex]]
-[[Category: Transferase-rna complex]]
-[[Category: Trna]]

4x4t: Difference between revisions

Revision as of 21:12, 12 April 2023

Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in CCACCA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools