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| | ==Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with ATP== | | ==Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with ATP== |
| - | <StructureSection load='2cja' size='340' side='right' caption='[[2cja]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='2cja' size='340' side='right'caption='[[2cja]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2cja]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Metbf Metbf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CJA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CJA FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2cja]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_barkeri_str._Fusaro Methanosarcina barkeri str. Fusaro]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CJA 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.2Å</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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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">[[2cim|2cim]], [[2cj9|2cj9]], [[2cjb|2cjb]]</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=2cja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cja OCA], [https://pdbe.org/2cja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cja RCSB], [https://www.ebi.ac.uk/pdbsum/2cja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cja ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] </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=2cja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cja OCA], [http://pdbe.org/2cja PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2cja RCSB], [http://www.ebi.ac.uk/pdbsum/2cja PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2cja ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/SYS2_METBF SYS2_METBF] Catalyzes the attachment of serine to tRNA(Ser). Is also probably able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).<ref>PMID:15364939</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]] | + | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Metbf]] | + | [[Category: Large Structures]] |
| - | [[Category: Serine--tRNA ligase]] | + | [[Category: Methanosarcina barkeri str. Fusaro]] |
| - | [[Category: Ahel, D]] | + | [[Category: Ahel D]] |
| - | [[Category: Ban, N]] | + | [[Category: Ban N]] |
| - | [[Category: Bilokapic, S]] | + | [[Category: Bilokapic S]] |
| - | [[Category: Gruic-Sovulj, I]] | + | [[Category: Gruic-Sovulj I]] |
| - | [[Category: Maier, T]] | + | [[Category: Maier T]] |
| - | [[Category: Soll, D]] | + | [[Category: Soll D]] |
| - | [[Category: Weygand-Durasevic, I]] | + | [[Category: Weygand-Durasevic I]] |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Trna synthetase]]
| + | |
| - | [[Category: Zinc ion]]
| + | |
| Structural highlights
2cja is a 2 chain structure with sequence from Methanosarcina barkeri str. Fusaro. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.2Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
SYS2_METBF Catalyzes the attachment of serine to tRNA(Ser). Is also probably able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec).[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
Methanogenic archaea possess unusual seryl-tRNA synthetase (SerRS), evolutionarily distinct from the SerRSs found in other archaea, eucaryotes and bacteria. The two types of SerRSs show only minimal sequence similarity, primarily within class II conserved motifs 1, 2 and 3. Here, we report a 2.5 A resolution crystal structure of the atypical methanogenic Methanosarcina barkeri SerRS and its complexes with ATP, serine and the nonhydrolysable seryl-adenylate analogue 5'-O-(N-serylsulfamoyl)adenosine. The structures reveal two idiosyncratic features of methanogenic SerRSs: a novel N-terminal tRNA-binding domain and an active site zinc ion. The tetra-coordinated Zn2+ ion is bound to three conserved protein ligands (Cys306, Glu355 and Cys461) and binds the amino group of the serine substrate. The absolute requirement of the metal ion for enzymatic activity was confirmed by mutational analysis of the direct zinc ion ligands. This zinc-dependent serine recognition mechanism differs fundamentally from the one employed by the bacterial-type SerRSs. Consequently, SerRS represents the only known aminoacyl-tRNA synthetase system that evolved two distinct mechanisms for the recognition of the same amino-acid substrate.
Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition.,Bilokapic S, Maier T, Ahel D, Gruic-Sovulj I, Soll D, Weygand-Durasevic I, Ban N EMBO J. 2006 Jun 7;25(11):2498-509. Epub 2006 May 4. PMID:16675947[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Korencic D, Polycarpo C, Weygand-Durasevic I, Söll D. Differential modes of transfer RNASer recognition in Methanosarcina barkeri. J Biol Chem. 2004 Nov 19;279(47):48780-6. PMID:15364939 doi:10.1074/jbc.M408753200
- ↑ Bilokapic S, Maier T, Ahel D, Gruic-Sovulj I, Soll D, Weygand-Durasevic I, Ban N. Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition. EMBO J. 2006 Jun 7;25(11):2498-509. Epub 2006 May 4. PMID:16675947
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