1b8a: Difference between revisions

Latest revision as of 05:37, 9 August 2023

ASPARTYL-TRNA SYNTHETASE

Structural highlights

1b8a is a 2 chain structure with sequence from Thermococcus kodakarensis KOD1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	ATP, MN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SYD_THEKO Catalyzes the attachment of L-aspartate to tRNA(Asp) in a two-step reaction: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp). Is specific for tRNA(Asp) since it aspartylates tRNA(Asn) 3 orders of magnitude less efficiently than tRNA(Asp).^[1] ^[2] ^[3]

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

The crystal structure of aspartyl-tRNA synthetase (AspRS) from Pyrococcus kodakaraensis was solved at 1.9 A resolution. The sequence and three-dimensional structure of the catalytic domain are highly homologous to those of eukaryotic AspRSs. In contrast, the N-terminal domain, whose function is to bind the tRNA anticodon, is more similar to that of eubacterial enzymes. Its structure explains the unique property of archaeal AspRSs of accommodating both tRNAAsp and tRNAAsn. Soaking the apo-enzyme crystals with ATP and aspartic acid both separately and together allows the adenylate formation to be followed. Due to the asymmetry of the dimeric enzyme in the crystalline state, different steps of the reaction could be visualized within the same crystal. Four different states of the aspartic acid activation reaction could thus be characterized, revealing the functional correlation of the observed conformational changes. The binding of the amino acid substrate induces movement of two invariant loops which secure the position of the peptidyl moiety for adenylate formation. An unambiguous spatial and functional assignment of three magnesium ion cofactors can be made. This study shows the important role of residues present in both archaeal and eukaryotic AspRSs, but absent from the eubacterial enzymes.

Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation.,Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D EMBO J. 1998 Sep 1;17(17):5227-37. PMID:9724658^[4]

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

References

↑ Tumbula-Hansen D, Feng L, Toogood H, Stetter KO, Söll D. Evolutionary divergence of the archaeal aspartyl-tRNA synthetases into discriminating and nondiscriminating forms. J Biol Chem. 2002 Oct 4;277(40):37184-90. PMID:12149259 doi:10.1074/jbc.M204767200
↑ Charron C, Roy H, Blaise M, Giege R, Kern D. Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain. EMBO J. 2003 Apr 1;22(7):1632-43. PMID:12660169 doi:10.1093/emboj/cdg148
↑ Feng L, Tumbula-Hansen D, Toogood H, Soll D. Expanding tRNA recognition of a tRNA synthetase by a single amino acid change. Proc Natl Acad Sci U S A. 2003 May 13;100(10):5676-81. PMID:12730374 doi:10.1073/pnas.0631525100
↑ Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D. Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J. 1998 Sep 1;17(17):5227-37. PMID:9724658 doi:10.1093/emboj/17.17.5227

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Tumbula-Hansen D, Feng L, Toogood H, Stetter KO, Söll D. Evolutionary divergence of the archaeal aspartyl-tRNA synthetases into discriminating and nondiscriminating forms. J Biol Chem. 2002 Oct 4;277(40):37184-90. PMID:12149259 doi:10.1074/jbc.M204767200

[2] Charron C, Roy H, Blaise M, Giege R, Kern D. Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain. EMBO J. 2003 Apr 1;22(7):1632-43. PMID:12660169 doi:10.1093/emboj/cdg148

[3] Feng L, Tumbula-Hansen D, Toogood H, Soll D. Expanding tRNA recognition of a tRNA synthetase by a single amino acid change. Proc Natl Acad Sci U S A. 2003 May 13;100(10):5676-81. PMID:12730374 doi:10.1073/pnas.0631525100

[4] Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D. Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J. 1998 Sep 1;17(17):5227-37. PMID:9724658 doi:10.1093/emboj/17.17.5227

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[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <StructureSection load='1b8a' size='340' side='right'caption='[[1b8a]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1b8a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B8A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1B8A FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1b8a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B8A FirstGlance]. <br>
-</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=MN:MANGANESE+(II)+ION'>MN</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]] 1.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ASPS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate--tRNA_ligase Aspartate--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.12 6.1.1.12] </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=1b8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b8a OCA], [https://pdbe.org/1b8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b8a RCSB], [https://www.ebi.ac.uk/pdbsum/1b8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b8a ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1b8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b8a OCA], [http://pdbe.org/1b8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b8a RCSB], [http://www.ebi.ac.uk/pdbsum/1b8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1b8a ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYD_THEKO SYD_THEKO] Catalyzes the attachment of L-aspartate to tRNA(Asp) in a two-step reaction: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp). Is specific for tRNA(Asp) since it aspartylates tRNA(Asn) 3 orders of magnitude less efficiently than tRNA(Asp).<ref>PMID:12149259</ref> <ref>PMID:12660169</ref> <ref>PMID:12730374</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Aspartate--tRNA ligase]]
 [[Category: Large Structures]]
-[[Category: Moras, D]]
+[[Category: Thermococcus kodakarensis KOD1]]
-[[Category: Moulinier, L]]
+[[Category: Moras D]]
-[[Category: Schmitt, E]]
+[[Category: Moulinier L]]
-[[Category: Thierry, J C]]
+[[Category: Schmitt E]]
-[[Category: Ligase]]
+[[Category: Thierry J-C]]
-[[Category: Synthetase]]
-[[Category: Trna ligase]]

1b8a: Difference between revisions

Latest revision as of 05:37, 9 August 2023

ASPARTYL-TRNA SYNTHETASE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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