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4kr6

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Revision as of 09:08, 7 December 2022

Crystal structure of a 4-thiouridine synthetase - RNA complex

Structural highlights

4kr6 is a 4 chain structure with sequence from Thermotoga maritima MSB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

THII_THEMA Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS (By similarity).

Publication Abstract from PubMed

In prokaryotes and archaea transfer ribonucleic acid (tRNA) stability as well as cellular UV protection relies on the post-transcriptional modification of uracil at position 8 (U8) of tRNAs by the 4-thiouridine synthetase ThiI. Here, we report three crystal structures of ThiI from Thermotoga maritima in complex with a truncated tRNA. The RNA is mainly bound by the N-terminal ferredoxin-like domain (NFLD) and the THUMP domain of one subunit within the ThiI homo-dimer thereby positioning the U8 close to the catalytic center in the pyrophosphatase domain of the other subunit. The recognition of the 3'-CCA end by the THUMP domain yields a molecular ruler defining the specificity for U8 thiolation. This first structure of a THUMP/NFLD-RNA complex might serve as paradigm for the RNA recognition by THUMP domains of other proteins. The ternary ThiI-RNA-ATP complex shows no significant structural changes due to adenosine triphosphate (ATP) binding, but two different states of active site loops are observed independent of the nucleotide loading state. Thereby conformational changes of the active site are coupled with conformational changes of the bound RNA. The ThiI-RNA complex structures indicate that full-length tRNA has to adopt a non-canonical conformation upon binding to ThiI.

Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification.,Neumann P, Lakomek K, Naumann PT, Erwin WM, Lauhon CT, Ficner R Nucleic Acids Res. 2014 Apr 5. PMID:24705700^[1]

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

References

↑ Neumann P, Lakomek K, Naumann PT, Erwin WM, Lauhon CT, Ficner R. Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification. Nucleic Acids Res. 2014 Apr 5. PMID:24705700 doi:http://dx.doi.org/10.1093/nar/gku249

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4kr6"

Categories: Large Structures | Thermotoga maritima MSB8 | Ficner R | Lakomek K | Neumann P

@@ Line 1: / Line 1: @@
 ==Crystal structure of a 4-thiouridine synthetase - RNA complex==
-<StructureSection load='4kr6' size='340' side='right' caption='[[4kr6]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
+<StructureSection load='4kr6' size='340' side='right'caption='[[4kr6]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4kr6]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KR6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KR6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4kr6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KR6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4kr7|4kr7]], [[4kr9|4kr9]]</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=4kr6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kr6 OCA], [https://pdbe.org/4kr6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kr6 RCSB], [https://www.ebi.ac.uk/pdbsum/4kr6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kr6 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AAD36761, thiI, TM_1694 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_sulfurtransferase tRNA sulfurtransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.8.1.4 2.8.1.4] </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=4kr6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kr6 OCA], [http://pdbe.org/4kr6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kr6 RCSB], [http://www.ebi.ac.uk/pdbsum/4kr6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kr6 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/THII_THEMA THII_THEMA]] Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS (By similarity).
+[https://www.uniprot.org/uniprot/THII_THEMA THII_THEMA] Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS (By similarity).
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Thema]]
+[[Category: Large Structures]]
-[[Category: TRNA sulfurtransferase]]
+[[Category: Thermotoga maritima MSB8]]
-[[Category: Ficner, R]]
+[[Category: Ficner R]]
-[[Category: Lakomek, K]]
+[[Category: Lakomek K]]
-[[Category: Neumann, P]]
+[[Category: Neumann P]]
-[[Category: 4-thiouridine synthesis]]
-[[Category: Adenylation]]
-[[Category: Pp-loop motif]]
-[[Category: Sulfurtransferase]]
-[[Category: Thiouridine]]
-[[Category: Thump domain]]
-[[Category: Transferase-rna complex]]
-[[Category: Trna modification]]

4kr6

From Proteopedia

Revision as of 09:08, 7 December 2022

Crystal structure of a 4-thiouridine synthetase - RNA complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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