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3aje

From Proteopedia

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Current revision

Crystal structure of S. tokodaii Sua5 complexed with L-threonine and AMPPNP

Structural highlights

3aje is a 1 chain structure with sequence from Sulfurisphaera tokodaii str. 7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SUA5_SULTO Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine (By similarity). Probably catalyzes the conversion of L-threonine, bicarbonate/CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of pyrophosphate. Shows ATP hydrolysis activity in vitro, producing AMP.^[1]

Publication Abstract from PubMed

The hypermodified nucleoside N(6)-threonylcarbamoyladenosine resides at position 37 of tRNA molecules bearing U at position 36 and maintains translational fidelity in the three kingdoms of life. The N(6)-threonylcarbamoyl moiety is composed of L-threonine and bicarbonate, and its synthesis was genetically shown to require YrdC/Sua5. YrdC/Sua5 binds to tRNA and ATP. In this study, we analyzed the L-threonine-binding mode of Sua5 from the archaeon Sulfolobus tokodaii. Isothermal titration calorimetry measurements revealed that S. tokodaii Sua5 binds L-threonine more strongly than L-serine and glycine. The Kd values of Sua5 for L-threonine and L-serine are 9.3 muM and 2.6 mM, respectively. We determined the crystal structure of S. tokodaii Sua5, complexed with AMPPNP and L-threonine, at 1.8 A resolution. The L-threonine is bound next to AMPPNP in the same pocket of the N-terminal domain. Thr118 and two water molecules form hydrogen bonds with AMPPNP in a unique manner for adenine-specific recognition. The carboxyl group and the side-chain hydroxyl and methyl groups of L-threonine are buried deep in the pocket, whereas the amino group faces AMPPNP. The L-threonine is located in a suitable position to react together with ATP for the synthesis of N(6)-threonylcarbamoyladenosine.

Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP.,Kuratani M, Kasai T, Akasaka R, Higashijima K, Terada T, Kigawa T, Shinkai A, Bessho Y, Yokoyama S Proteins. 2011 Jul;79(7):2065-75. doi: 10.1002/prot.23026. Epub 2011 May 2. PMID:21538543^[2]

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

References

↑ Parthier C, Gorlich S, Jaenecke F, Breithaupt C, Brauer U, Fandrich U, Clausnitzer D, Wehmeier UF, Bottcher C, Scheel D, Stubbs MT. The O-Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction. Angew Chem Int Ed Engl. 2012 Mar 1. doi: 10.1002/anie.201108896. PMID:22383337 doi:10.1002/anie.201108896
↑ Kuratani M, Kasai T, Akasaka R, Higashijima K, Terada T, Kigawa T, Shinkai A, Bessho Y, Yokoyama S. Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP. Proteins. 2011 Jul;79(7):2065-75. doi: 10.1002/prot.23026. Epub 2011 May 2. PMID:21538543 doi:http://dx.doi.org/10.1002/prot.23026

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/3aje"

Categories: Large Structures | Sulfurisphaera tokodaii str. 7 | Kuratani M | Yokoyama S

@@ Line 3: / Line 3: @@
 <StructureSection load='3aje' size='340' side='right'caption='[[3aje]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3aje]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulto Sulto]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AJE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AJE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3aje]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AJE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AJE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=THR:THREONINE'>THR</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]] 1.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2eqa|2eqa]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=THR:THREONINE'>THR</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ST1526 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273063 SULTO])</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=3aje FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aje OCA], [https://pdbe.org/3aje PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3aje RCSB], [https://www.ebi.ac.uk/pdbsum/3aje PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3aje ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/SUA5_SULTO SUA5_SULTO]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine (By similarity). Probably catalyzes the conversion of L-threonine, bicarbonate/CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of pyrophosphate. Shows ATP hydrolysis activity in vitro, producing AMP.<ref>PMID:22383337</ref>
+[https://www.uniprot.org/uniprot/SUA5_SULTO SUA5_SULTO] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine (By similarity). Probably catalyzes the conversion of L-threonine, bicarbonate/CO(2) and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of pyrophosphate. Shows ATP hydrolysis activity in vitro, producing AMP.<ref>PMID:22383337</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Sulto]]
+[[Category: Sulfurisphaera tokodaii str. 7]]
-[[Category: Kuratani, M]]
+[[Category: Kuratani M]]
-[[Category: Structural genomic]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S]]
-[[Category: Rna binding protein]]
-[[Category: Rsgi]]
-[[Category: Trna modification t6a]]

3aje

From Proteopedia

Current revision

Crystal structure of S. tokodaii Sua5 complexed with L-threonine and AMPPNP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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