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4rdh

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Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA

Structural highlights

4rdh is a 4 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TCDA_ECOLI Catalyzes the ATP-dependent dehydration of threonylcarbamoyladenosine at position 37 (t(6)A37) to form cyclic t(6)A37 (ct(6)A37) in tRNAs that read codons beginning with adenine. TcdA is also part of a sulfur transfer pathway; is able to accept sulfur from CsdA directly in vitro, but CsdE might act as the sulfur donor in vivo.^[1] ^[2]

Publication Abstract from PubMed

Escherichia coli TcdA (also known as CsdL) was previously shown to catalyze the ATP-dependent dehydration/cyclization of hypermodified tRNA N6-threonylcarbamoyladenosine into further cyclic N6-threonylcarbamoyladenosine. In this study, we report the X-ray crystal structures of E. coli TcdA with either AMP or ATP bound. The AMP/ATP-bound N-terminal sub-domain of TcdA resembles the ATP-binding Rossmann fold of E. coli ThiF and MoeB that are enzymes respectively taking part in the biosynthesis of thiamine and molybdopterin; however, the remaining C-terminal sub-domain of TcdA adopts a structure unrelated to any other known folds. In TcdA, the ATP-utilizing adenylation of tRNA N6-threonylcarbamoyladenosine and a subsequent thioester formation via an active cysteine, similar to the mechanisms in ThiF and MoeB, could take place for the dehydratase function. Analysis of the structure with sequence alignment suggests the disordered Cys234 of TcdA as the most likely catalytic residue. The structure further indicates that the C-terminal sub-domain can provide a binding interface for the tRNA substrate. Binding study using the surface mutants of TcdA and tRNA reveals that the positively charged regions of mainly the C-terminal sub-domain are important for the tRNA recognition.

The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N-Threonylcarbamoyladenosine Dehydratase Activity.,Kim S, Lee H, Park S J Mol Biol. 2015 Jun 21. pii: S0022-2836(15)00345-9. doi:, 10.1016/j.jmb.2015.06.005. PMID:26101842^[3]

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

References

↑ Trotter V, Vinella D, Loiseau L, Ollagnier de Choudens S, Fontecave M, Barras F. The CsdA cysteine desulphurase promotes Fe/S biogenesis by recruiting Suf components and participates to a new sulphur transfer pathway by recruiting CsdL (ex-YgdL), a ubiquitin-modifying-like protein. Mol Microbiol. 2009 Dec;74(6):1527-42. PMID:20054882
↑ Miyauchi K, Kimura S, Suzuki T. A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. Nat Chem Biol. 2013 Feb;9(2):105-11. doi: 10.1038/nchembio.1137. Epub 2012 Dec, 16. PMID:23242255 doi:http://dx.doi.org/10.1038/nchembio.1137
↑ Kim S, Lee H, Park S. The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N-Threonylcarbamoyladenosine Dehydratase Activity. J Mol Biol. 2015 Jun 21. pii: S0022-2836(15)00345-9. doi:, 10.1016/j.jmb.2015.06.005. PMID:26101842 doi:http://dx.doi.org/10.1016/j.jmb.2015.06.005

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/4rdh"

Categories: Escherichia coli | Large Structures | Kim S | Lee H | Park SY

@@ Line 1: / Line 1: @@
 ==Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA==
-<StructureSection load='4rdh' size='340' side='right' caption='[[4rdh]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='4rdh' size='340' side='right'caption='[[4rdh]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4rdh]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RDH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4rdh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RDH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RDH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.1&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4rdi|4rdi]]</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=4rdh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rdh OCA], [https://pdbe.org/4rdh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rdh RCSB], [https://www.ebi.ac.uk/pdbsum/4rdh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rdh ProSAT]</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=4rdh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rdh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rdh RCSB], [http://www.ebi.ac.uk/pdbsum/4rdh PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TCDA_ECOLI TCDA_ECOLI]] Catalyzes the ATP-dependent dehydration of threonylcarbamoyladenosine at position 37 (t(6)A37) to form cyclic t(6)A37 (ct(6)A37) in tRNAs that read codons beginning with adenine. TcdA is also part of a sulfur transfer pathway; is able to accept sulfur from CsdA directly in vitro, but CsdE might act as the sulfur donor in vivo.<ref>PMID:20054882</ref> <ref>PMID:23242255</ref>
+[https://www.uniprot.org/uniprot/TCDA_ECOLI TCDA_ECOLI] Catalyzes the ATP-dependent dehydration of threonylcarbamoyladenosine at position 37 (t(6)A37) to form cyclic t(6)A37 (ct(6)A37) in tRNAs that read codons beginning with adenine. TcdA is also part of a sulfur transfer pathway; is able to accept sulfur from CsdA directly in vitro, but CsdE might act as the sulfur donor in vivo.<ref>PMID:20054882</ref> <ref>PMID:23242255</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4rdh" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Kim, S]]
+[[Category: Escherichia coli]]
-[[Category: Lee, H]]
+[[Category: Large Structures]]
-[[Category: Park, S Y]]
+[[Category: Kim S]]
-[[Category: Dehydratase]]
+[[Category: Lee H]]
-[[Category: Ligase]]
+[[Category: Park SY]]
-[[Category: Rossmann fold]]

4rdh

From Proteopedia

Current revision

Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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