2dlc

From Proteopedia

(Difference between revisions)

Revision as of 10:32, 8 December 2021

Crystal structure of the ternary complex of yeast tyrosyl-tRNA synthetase

Structural highlights

2dlc is a 2 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:	, , , , , , , ,
Activity:	Tyrosine--tRNA ligase, with EC number 6.1.1.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SYYC_YEAST] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). The specificity determinants on tRNA(Tyr) are the base pair C1-G72, the discriminator residue A73, and the three anticodon bases G34, U35 and A36. Also involved in nuclear tRNA export.^[1] ^[2]

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 specific aminoacylation of tRNA by tyrosyl-tRNA synthetases (TyrRSs) relies on the identity determinants in the cognate tRNA(Tyr)s. We have determined the crystal structure of Saccharomyces cerevisiae TyrRS (SceTyrRS) complexed with a Tyr-AMP analog and the native tRNA(Tyr)(GPsiA). Structural information for TyrRS-tRNA(Tyr) complexes is now full-line for three kingdoms. Because the archaeal/eukaryotic TyrRSs-tRNA(Tyr)s pairs do not cross-react with their bacterial counterparts, the recognition modes of the identity determinants by the archaeal/eukaryotic TyrRSs were expected to be similar to each other but different from that by the bacterial TyrRSs. Interestingly, however, the tRNA(Tyr) recognition modes of SceTyrRS have both similarities and differences compared with those in the archaeal TyrRS: the recognition of the C1-G72 base pair by SceTyrRS is similar to that by the archaeal TyrRS, whereas the recognition of the A73 by SceTyrRS is different from that by the archaeal TyrRS but similar to that by the bacterial TyrRS. Thus, the lack of cross-reactivity between archaeal/eukaryotic and bacterial TyrRS-tRNA(Tyr) pairs most probably lies in the different sequence of the last base pair of the acceptor stem (C1-G72 vs G1-C72) of tRNA(Tyr). On the other hand, the recognition mode of Tyr-AMP is conserved among the TyrRSs from the three kingdoms.

Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms.,Tsunoda M, Kusakabe Y, Tanaka N, Ohno S, Nakamura M, Senda T, Moriguchi T, Asai N, Sekine M, Yokogawa T, Nishikawa K, Nakamura KT Nucleic Acids Res. 2007;35(13):4289-300. Epub 2007 Jun 18. PMID:17576676^[3]

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

References

↑ Sarkar S, Azad AK, Hopper AK. Nuclear tRNA aminoacylation and its role in nuclear export of endogenous tRNAs in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14366-71. PMID:10588711
↑ Fechter P, Rudinger-Thirion J, Theobald-Dietrich A, Giege R. Identity of tRNA for yeast tyrosyl-tRNA synthetase: tyrosylation is more sensitive to identity nucleotides than to structural features. Biochemistry. 2000 Feb 22;39(7):1725-33. PMID:10677221
↑ Tsunoda M, Kusakabe Y, Tanaka N, Ohno S, Nakamura M, Senda T, Moriguchi T, Asai N, Sekine M, Yokogawa T, Nishikawa K, Nakamura KT. Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms. Nucleic Acids Res. 2007;35(13):4289-300. Epub 2007 Jun 18. PMID:17576676 doi:http://dx.doi.org/10.1093/nar/gkm417

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2dlc"

@@ Line 3: / Line 3: @@
 <StructureSection load='2dlc' size='340' side='right'caption='[[2dlc]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2dlc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DLC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DLC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2dlc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DLC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DLC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=YMP:O-(ADENOSINE-5-O-YL)-N-(L-TYROSYL)PHOSPHORAMIDATE'>YMP</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=YMP:O-(ADENOSINE-5-O-YL)-N-(L-TYROSYL)PHOSPHORAMIDATE'>YMP</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=6IA:N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>6IA</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </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=2dlc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dlc OCA], [http://pdbe.org/2dlc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dlc RCSB], [http://www.ebi.ac.uk/pdbsum/2dlc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dlc 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=2dlc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dlc OCA], [https://pdbe.org/2dlc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dlc RCSB], [https://www.ebi.ac.uk/pdbsum/2dlc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dlc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SYYC_YEAST SYYC_YEAST]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). The specificity determinants on tRNA(Tyr) are the base pair C1-G72, the discriminator residue A73, and the three anticodon bases G34, U35 and A36. Also involved in nuclear tRNA export.<ref>PMID:10588711</ref> <ref>PMID:10677221</ref>
+[[https://www.uniprot.org/uniprot/SYYC_YEAST SYYC_YEAST]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). The specificity determinants on tRNA(Tyr) are the base pair C1-G72, the discriminator residue A73, and the three anticodon bases G34, U35 and A36. Also involved in nuclear tRNA export.<ref>PMID:10588711</ref> <ref>PMID:10677221</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

2dlc

From Proteopedia

Revision as of 10:32, 8 December 2021

Crystal structure of the ternary complex of yeast tyrosyl-tRNA synthetase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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