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| | ==Leishmania donovani tyrosyl-tRNA synthetase in complex with nanobody and inhibitor== | | ==Leishmania donovani tyrosyl-tRNA synthetase in complex with nanobody and inhibitor== |
| - | <StructureSection load='5usf' size='340' side='right' caption='[[5usf]], [[Resolution|resolution]] 2.75Å' scene=''> | + | <StructureSection load='5usf' size='340' side='right'caption='[[5usf]], [[Resolution|resolution]] 2.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5usf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_glama Camelus glama] and [http://en.wikipedia.org/wiki/Leidb Leidb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5USF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5USF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5usf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Lama_glama Lama glama] and [https://en.wikipedia.org/wiki/Leishmania_donovani_BPK282A1 Leishmania donovani BPK282A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5USF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5USF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</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]] 2.75Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LDBPK_141460 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=981087 LEIDB])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YSA:5-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE'>YSA</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=5usf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5usf OCA], [http://pdbe.org/5usf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5usf RCSB], [http://www.ebi.ac.uk/pdbsum/5usf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5usf ProSAT]</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=5usf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5usf OCA], [https://pdbe.org/5usf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5usf RCSB], [https://www.ebi.ac.uk/pdbsum/5usf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5usf ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A0A3Q8ID88_LEIDO A0A3Q8ID88_LEIDO] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Camelus glama]] | + | [[Category: Lama glama]] |
| - | [[Category: Leidb]] | + | [[Category: Large Structures]] |
| - | [[Category: Barros-Alvarez, X]] | + | [[Category: Leishmania donovani BPK282A1]] |
| - | [[Category: Hol, W G.J]] | + | [[Category: Barros-Alvarez X]] |
| - | [[Category: Inhibitor]]
| + | [[Category: Hol WGJ]] |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Ligase-ligase inhibitor complex]]
| + | |
| - | [[Category: Synthetase]] | + | |
| - | [[Category: Tyrosine]]
| + | |
| - | [[Category: Tyrosyl-adenylate analog]]
| + | |
| Structural highlights
Function
A0A3Q8ID88_LEIDO
Publication Abstract from PubMed
The crystal structure of Leishmania donovani tyrosyl-tRNA synthetase (LdTyrRS) in complex with a nanobody and the tyrosyl adenylate analog TyrSA was determined at 2.75 A resolution. Nanobodies are the variable domains of camelid heavy chain-only antibodies. The nanobody makes numerous crystal contacts and in addition reduces the flexibility of a loop of LdTyrRS. TyrSA is engaged in many interactions with active site residues occupying the tyrosine and adenine binding pockets. The LdTyrRS polypeptide chain consists of two pseudo-monomers, each consisting of two domains. Comparing the two independent chains in the asymmetric unit reveals that the two pseudo-monomers of LdTyrRS can bend with respect to each other essentially as rigid bodies. This flexibility might be useful in the positioning of tRNA for catalysis since both pseudo-monomers in the LdTyrRS chain are needed for charging tRNATyr. An "extra pocket" (EP) appears to be present near the adenine binding region of LdTyrRS. Since this pocket is absent in the two human homologous enzymes, the EP provides interesting opportunities for obtaining selective drugs for treating infections caused by L. donovani, a unicellular parasite causing visceral leishmaniasis, or kala azar, which claims 20,000 to 30,000 deaths per year. Sequence and structural comparisons indicate that the EP is a characteristic which also occurs in the active site of several other important pathogenic protozoa. Therefore, the structure of LdTyrRS could inspire the design of compounds useful for treating several different parasitic diseases.
Leishmania donovani tyrosyl-tRNA synthetase structure in complex with a tyrosyl adenylate analog and comparisons with human and protozoan counterparts.,Barros-Alvarez X, Kerchner KM, Koh CY, Turley S, Pardon E, Steyaert J, Ranade RM, Gillespie JR, Zhang Z, Verlinde CLMJ, Fan E, Buckner FS, Hol WGJ Biochimie. 2017 Apr 17. pii: S0300-9084(17)30100-1. doi:, 10.1016/j.biochi.2017.04.006. PMID:28427904[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Barros-Alvarez X, Kerchner KM, Koh CY, Turley S, Pardon E, Steyaert J, Ranade RM, Gillespie JR, Zhang Z, Verlinde CLMJ, Fan E, Buckner FS, Hol WGJ. Leishmania donovani tyrosyl-tRNA synthetase structure in complex with a tyrosyl adenylate analog and comparisons with human and protozoan counterparts. Biochimie. 2017 Apr 17. pii: S0300-9084(17)30100-1. doi:, 10.1016/j.biochi.2017.04.006. PMID:28427904 doi:http://dx.doi.org/10.1016/j.biochi.2017.04.006
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