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| | ==E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP== | | ==E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP== |
| - | <StructureSection load='4wq4' size='340' side='right' caption='[[4wq4]], [[Resolution|resolution]] 2.33Å' scene=''> | + | <StructureSection load='4wq4' size='340' side='right'caption='[[4wq4]], [[Resolution|resolution]] 2.33Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4wq4]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WQ4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4wq4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WQ4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N(6)-L-threonylcarbamoyladenine_synthase N(6)-L-threonylcarbamoyladenine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.99.4 2.6.99.4] </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=4wq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wq4 OCA], [https://pdbe.org/4wq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wq4 RCSB], [https://www.ebi.ac.uk/pdbsum/4wq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wq4 ProSAT]</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=4wq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wq4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wq4 RCSB], [http://www.ebi.ac.uk/pdbsum/4wq4 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TSAD_ECOLI TSAD_ECOLI]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. May also be involved in the metabolism of glycated proteins, but does not show sialoglycoprotease activity against glycophorin A.<ref>PMID:20824107</ref> <ref>PMID:21183954</ref> <ref>PMID:22378793</ref> [[http://www.uniprot.org/uniprot/TSAB_ECOLI TSAB_ECOLI]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD. In fact, can act as a protease that specifically degrades TsaD in vitro; therefore TsaB may post-translationally regulate cellular pools of TsaD via proteolytic degradation. Does not show sialoglycoprotease activity against glycophorin A.<ref>PMID:19376873</ref> <ref>PMID:22378793</ref> | + | [https://www.uniprot.org/uniprot/TSAD_ECOLI TSAD_ECOLI] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. May also be involved in the metabolism of glycated proteins, but does not show sialoglycoprotease activity against glycophorin A.<ref>PMID:20824107</ref> <ref>PMID:21183954</ref> <ref>PMID:22378793</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4wq4" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Collinet, B]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Zhang, W]] | + | [[Category: Large Structures]] |
| - | [[Category: Glu12ala]] | + | [[Category: Collinet B]] |
| - | [[Category: Heterodimer]] | + | [[Category: Zhang W]] |
| - | [[Category: T6a]]
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| - | [[Category: Transferase]]
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| - | [[Category: Ygjd-yeaz]]
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| Structural highlights
Function
TSAD_ECOLI Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. May also be involved in the metabolism of glycated proteins, but does not show sialoglycoprotease activity against glycophorin A.[1] [2] [3]
Publication Abstract from PubMed
The essential and universal N6-threonylcarbamoyladenosine (t6A) modification at position 37 of ANN-decoding tRNAs plays a pivotal role in translational fidelity through enhancement of the cognate codon recognition and stabilization of the codon-anticodon interaction. In Escherichia coli, the YgjD (TsaD), YeaZ (TsaB), YjeE (TsaE) and YrdC (TsaC) proteins are necessary and sufficient for the in vitro biosynthesis of t6A, using tRNA, ATP, L-threonine and bicarbonate as substrates. YrdC synthesizes the short-lived L-threonylcarbamoyladenylate (TCA), and YgjD, YeaZ and YjeE cooperate to transfer the L-threonylcarbamoyl-moiety from TCA onto adenosine at position 37 of substrate tRNA. We determined the crystal structure of the heterodimer YgjD-YeaZ at 2.3 A, revealing the presence of an unexpected molecule of ADP bound at an atypical site situated at the YgjD-YeaZ interface. We further showed that the ATPase activity of YjeE is strongly activated by the YgjD-YeaZ heterodimer. We established by binding experiments and SAXS data analysis that YgjD-YeaZ and YjeE form a compact ternary complex only in presence of ATP. The formation of the ternary YgjD-YeaZ-YjeE complex is required for the in vitro biosynthesis of t6A but not its ATPase activity.
The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli.,Zhang W, Collinet B, Perrochia L, Durand D, van Tilbeurgh H Nucleic Acids Res. 2015 Jan 10. pii: gku1397. PMID:25578970[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Katz C, Cohen-Or I, Gophna U, Ron EZ. The ubiquitous conserved glycopeptidase Gcp prevents accumulation of toxic glycated proteins. MBio. 2010 Aug 24;1(3). pii: e00195-10. doi: 10.1128/mBio.00195-10. PMID:20824107 doi:http://dx.doi.org/10.1128/mBio.00195-10
- ↑ Srinivasan M, Mehta P, Yu Y, Prugar E, Koonin EV, Karzai AW, Sternglanz R. The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A. EMBO J. 2011 Mar 2;30(5):873-81. doi: 10.1038/emboj.2010.343. Epub 2010 Dec 24. PMID:21183954 doi:10.1038/emboj.2010.343
- ↑ Deutsch C, El Yacoubi B, de Crecy-Lagard V, Iwata-Reuyl D. Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J Biol Chem. 2012 Apr 20;287(17):13666-73. doi: 10.1074/jbc.M112.344028. Epub, 2012 Feb 29. PMID:22378793 doi:http://dx.doi.org/10.1074/jbc.M112.344028
- ↑ Zhang W, Collinet B, Perrochia L, Durand D, van Tilbeurgh H. The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli. Nucleic Acids Res. 2015 Jan 10. pii: gku1397. PMID:25578970 doi:http://dx.doi.org/10.1093/nar/gku1397
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