4d79

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA, in complex with ATP at 1.768 Angstroem resolution

Structural highlights

4d79 is a 4 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.768Å
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

Cyclic N6-threonylcarbamoyladenosine ('cyclic t6A', ct6A) is a non-thiolated hypermodification found in transfer RNAs (tRNAs) in bacteria, protists, fungi and plants. In bacteria and yeast cells ct6A has been shown to enhance translation fidelity and efficiency of ANN codons by improving the faithful discrimination of aminoacylated tRNAs by the ribosome. To further the understanding of ct6A biology we have determined the high-resolution crystal structures of CsdL/TcdA in complex with AMP and ATP, an E1-like activating enzyme from Escherichia coli, which catalyzes the ATP-dependent dehydration of t6A to form ct6A. CsdL/TcdA is a dimer whose structural integrity and dimer interface depend critically on strongly bound K+ and Na+ cations. By using biochemical assays and small-angle X-ray scattering we show that CsdL/TcdA can associate with tRNA with a 1:1 stoichiometry and with the proper position and orientation for the cyclization of t6A. Furthermore, we show by nuclear magnetic resonance that CsdL/TcdA engages in transient interactions with CsdA and CsdE, which, in the latter case, involve catalytically important residues. These short-lived interactions may underpin the precise channeling of sulfur atoms from cysteine to CsdL/TcdA as previously characterized. In summary, the combination of structural, biophysical and biochemical methods applied to CsdL/TcdA has afforded a more thorough understanding of how the structure of this E1-like enzyme has been fine tuned to accomplish ct6A synthesis on tRNAs while providing support for the notion that CsdA and CsdE are able to functionally interact with CsdL/TcdA.

The Crystal Structure and Small-Angle X-Ray Analysis of CsdL/TcdA Reveal a New tRNA Binding Motif in the MoeB/E1 Superfamily.,Lopez-Estepa M, Arda A, Savko M, Round A, Shepard WE, Bruix M, Coll M, Fernandez FJ, Jimenez-Barbero J, Vega MC PLoS One. 2015 Apr 21;10(4):e0118606. doi: 10.1371/journal.pone.0118606., eCollection 2015. PMID:25897750^[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
↑ Lopez-Estepa M, Arda A, Savko M, Round A, Shepard WE, Bruix M, Coll M, Fernandez FJ, Jimenez-Barbero J, Vega MC. The Crystal Structure and Small-Angle X-Ray Analysis of CsdL/TcdA Reveal a New tRNA Binding Motif in the MoeB/E1 Superfamily. PLoS One. 2015 Apr 21;10(4):e0118606. doi: 10.1371/journal.pone.0118606., eCollection 2015. PMID:25897750 doi:http://dx.doi.org/10.1371/journal.pone.0118606

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/4d79"

@@ Line 1: / Line 1: @@
 ==Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA, in complex with ATP at 1.768 Angstroem resolution==
-<StructureSection load='4d79' size='340' side='right' caption='[[4d79]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
+<StructureSection load='4d79' size='340' side='right'caption='[[4d79]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4d79]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D79 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D79 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4d79]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D79 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.768&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4d7a|4d7a]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=4d79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d79 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d79 RCSB], [http://www.ebi.ac.uk/pdbsum/4d79 PDBsum]</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=4d79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d79 OCA], [https://pdbe.org/4d79 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d79 RCSB], [https://www.ebi.ac.uk/pdbsum/4d79 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d79 ProSAT]</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 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4d79" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arda, A]]
+[[Category: Escherichia coli K-12]]
-[[Category: Bruix, M]]
+[[Category: Large Structures]]
-[[Category: Coll, M]]
+[[Category: Arda A]]
-[[Category: Fernandez, F J]]
+[[Category: Bruix M]]
-[[Category: Jimenez-Barbero, J]]
+[[Category: Coll M]]
-[[Category: Lopez-Estepa, M]]
+[[Category: Fernandez FJ]]
-[[Category: Round, A]]
+[[Category: Jimenez-Barbero J]]
-[[Category: Savko, M]]
+[[Category: Lopez-Estepa M]]
-[[Category: Shepard, W]]
+[[Category: Round A]]
-[[Category: Vega, M C]]
+[[Category: Savko M]]
-[[Category: L-cysteine desulfurase]]
+[[Category: Shepard W]]
-[[Category: Ligase]]
+[[Category: Vega MC]]
-[[Category: Sulfur trafficking]]
-[[Category: Transpersulfuration]]

4d79

From Proteopedia

Current revision

Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA, in complex with ATP at 1.768 Angstroem resolution

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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