3a31

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix (selenomethionine derivative)

Structural highlights

3a31 is a 1 chain structure with sequence from Aeropyrum pernix. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SYTC_AERPE Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr) (Probable). This protein is probably not able to deacylate mischarged L-seryl-tRNA(Thr) as it lacks the appropriate domain (PubMed:19761773).^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

In protein synthesis, threonyl-tRNA synthetase (ThrRS) must recognize threonine (Thr) from the 20 kinds of amino acids and the cognate tRNA(Thr) from different tRNAs in order to generate Thr-tRNA(Thr). In general, an organism possesses one kind of gene corresponding to ThrRS. However, it has been recently found that some organisms have two different genes for ThrRS in the genome, suggesting that their proteins ThrRS-1 and ThrRS-2 function separately and complement each other in the threonylation of tRNA(Thr), one for catalysis and the other for trans-editing of misacylated Ser-tRNA(Thr). In order to clarify their three-dimensional structures, we performed X-ray analyses of two putatively assigned ThrRSs from Aeropyrum pernix (ApThrRS-1 and ApThrRS-2). These proteins were overexpressed in Escherichia coli, purified, and crystallized. The crystal structure of ApThrRS-1 has been successfully determined at 2.3 A resolution. ApThrRS-1 is a dimeric enzyme composed of two identical subunits, each containing two domains for the catalytic reaction and for anticodon binding. The essential editing domain is completely missing as expected. These structural features reveal that ThrRS-1 catalyzes only the aminoacylation of the cognate tRNA, suggesting the necessity of the second enzyme ThrRS-2 for trans-editing. Since the N-terminal sequence of ApThrRS-2 is similar to the sequence of the editing domain of ThrRS from Pyrococcus abyssi, ApThrRS-2 has been expected to catalyze deaminoacylation of a misacylated serine moiety at the CCA terminus.

Two complementary enzymes for threonylation of tRNA in crenarchaeota: crystal structure of Aeropyrum pernix threonyl-tRNA synthetase lacking a cis-editing domain.,Shimizu S, Juan EC, Sato Y, Miyashita Y, Hoque MM, Suzuki K, Sagara T, Tsunoda M, Sekiguchi T, Dock-Bregeon AC, Moras D, Takenaka A J Mol Biol. 2009 Nov 27;394(2):286-96. Epub 2009 Sep 15. PMID:19761773^[2]

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

References

↑ Shimizu S, Juan EC, Sato Y, Miyashita Y, Hoque MM, Suzuki K, Sagara T, Tsunoda M, Sekiguchi T, Dock-Bregeon AC, Moras D, Takenaka A. Two complementary enzymes for threonylation of tRNA in crenarchaeota: crystal structure of Aeropyrum pernix threonyl-tRNA synthetase lacking a cis-editing domain. J Mol Biol. 2009 Nov 27;394(2):286-96. Epub 2009 Sep 15. PMID:19761773 doi:10.1016/j.jmb.2009.09.018
↑ Shimizu S, Juan EC, Sato Y, Miyashita Y, Hoque MM, Suzuki K, Sagara T, Tsunoda M, Sekiguchi T, Dock-Bregeon AC, Moras D, Takenaka A. Two complementary enzymes for threonylation of tRNA in crenarchaeota: crystal structure of Aeropyrum pernix threonyl-tRNA synthetase lacking a cis-editing domain. J Mol Biol. 2009 Nov 27;394(2):286-96. Epub 2009 Sep 15. PMID:19761773 doi:10.1016/j.jmb.2009.09.018

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3a31"

@@ Line 3: / Line 3: @@
 <StructureSection load='3a31' size='340' side='right'caption='[[3a31]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3a31]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A31 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A31 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3a31]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A31 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A31 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.5&#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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a32|3a32]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APE0809.1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56636 AERPX])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Threonine--tRNA_ligase Threonine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.3 6.1.1.3] </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=3a31 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a31 OCA], [https://pdbe.org/3a31 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a31 RCSB], [https://www.ebi.ac.uk/pdbsum/3a31 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a31 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYTC_AERPE SYTC_AERPE] Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr) (Probable). This protein is probably not able to deacylate mischarged L-seryl-tRNA(Thr) as it lacks the appropriate domain (PubMed:19761773).<ref>PMID:19761773</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 16: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a3/3a31_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Aerpx]]
+[[Category: Aeropyrum pernix]]
 [[Category: Large Structures]]
-[[Category: Threonine--tRNA ligase]]
+[[Category: Dock-Bregeon A-C]]
-[[Category: Dock-Bregeon, A C]]
+[[Category: Hoque MM]]
-[[Category: Hoque, M M]]
+[[Category: Juan ECM]]
-[[Category: Juan, E C.M]]
+[[Category: Miyashita Y]]
-[[Category: Miyashita, Y]]
+[[Category: Moras D]]
-[[Category: Moras, D]]
+[[Category: Sato Y]]
-[[Category: Sato, Y]]
+[[Category: Sekiguchi T]]
-[[Category: Sekiguchi, T]]
+[[Category: Shimizu S]]
-[[Category: Shimizu, S]]
+[[Category: Suzuki K]]
-[[Category: Suzuki, K]]
+[[Category: Takenaka A]]
-[[Category: Takenaka, A]]
+[[Category: Tsunoda M]]
-[[Category: Tsunoda, M]]
+[[Category: Yogiashi M]]
-[[Category: Yogiashi, M]]
-[[Category: Aeropyrum pernix k1]]
-[[Category: Aminoacyl-trna synthetase]]
-[[Category: Atp-binding]]
-[[Category: Ligase]]
-[[Category: Metal-binding]]
-[[Category: Nucleotide-binding]]
-[[Category: Protein biosynthesis]]
-[[Category: Threonyl-trna synthetase]]

3a31

From Proteopedia

Current revision

Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix (selenomethionine derivative)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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