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3r6m

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<StructureSection load='3r6m' size='340' side='right'caption='[[3r6m]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
<StructureSection load='3r6m' size='340' side='right'caption='[[3r6m]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3r6m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"oceanomonas_parahaemolytica"_(fujino_et_al._1951)_miyamoto_et_al._1961 "oceanomonas parahaemolytica" (fujino et al. 1951) miyamoto et al. 1961]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R6M FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3r6m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_parahaemolyticus Vibrio parahaemolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R6M FirstGlance]. <br>
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</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VP0866, YeaZ ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=670 "Oceanomonas parahaemolytica" (Fujino et al. 1951) Miyamoto et al. 1961])</td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</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=3r6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6m OCA], [https://pdbe.org/3r6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r6m RCSB], [https://www.ebi.ac.uk/pdbsum/3r6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r6m 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=3r6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6m OCA], [https://pdbe.org/3r6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r6m RCSB], [https://www.ebi.ac.uk/pdbsum/3r6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r6m ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/TSAB_VIBPA TSAB_VIBPA]] 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 involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE; this reaction does not require ATP in vitro. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD (By similarity).
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[https://www.uniprot.org/uniprot/TSAB_VIBPA TSAB_VIBPA] 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 involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE; this reaction does not require ATP in vitro. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD (By similarity).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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BACKGROUND: The yeaZ gene product forms part of the conserved network YjeE/YeaZ/YgjD essential for the survival of many Gram-negative eubacteria. Among other as yet unidentified roles, YeaZ functions as a resuscitation promoting factor required for survival and resuscitation of cells in a viable but non-culturable (VBNC) state. METHODOLOGY/PRINCIPAL FINDINGS: In order to investigate in detail the structure/function relationship of this family of proteins we have performed X-ray crystallographic studies of Vibrio parahaemolyticus YeaZ. The YeaZ structure showed that it has a classic actin-like nucleotide-binding fold. Comparisons of this crystal structure to that of available homologues from E. coli, T. maritima and S. typhimurium revealed two distinctly different modes of dimer formation. In one form, prevalent in the absence of nucleotide, the putative nucleotide-binding site is incomplete, lacking a binding pocket for a nucleotide base. In the second form, residues from the second subunit complete the nucleotide-binding site. This suggests that the two dimer architectures observed in the crystal structures correspond to a free and a nucleotide-bound form of YeaZ. A multiple sequence alignment of YeaZ proteins from different bacteria allowed us to identify a large conserved hydrophobic patch on the protein surface that becomes exposed upon nucleotide-driven dimer re-arrangement. We hypothesize that the transition between two dimer architectures represents the transition between the 'on' and 'off' states of YeaZ. The effect of this transition is to alternately expose and bury a docking site for the partner protein YgjD. CONCLUSIONS/SIGNIFICANCE: This paper provides the first structural insight into the putative mechanism of nucleotide regulation of YeaZ through dimer reorganization. Our analysis suggests that nucleotide binding to YeaZ may act as a regulator or switch that changes YeaZ shape, allowing it to switch partners between YjeE and YgjD.
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Structural Analysis of the Essential Resuscitation Promoting Factor YeaZ Suggests a Mechanism of Nucleotide Regulation through Dimer Reorganization.,Aydin I, Saijo-Hamano Y, Namba K, Thomas C, Roujeinikova A PLoS One. 2011;6(8):e23245. Epub 2011 Aug 17. PMID:21858042<ref>PMID:21858042</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3r6m" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Aydin, I]]
 
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[[Category: Roujeinikova, A]]
 
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[[Category: Actin/hsp70 nucleotide-binding fold]]
 
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[[Category: Bacterial resuscitation]]
 
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[[Category: Hydrolase]]
 
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[[Category: Resuscitation promoting factor]]
 
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[[Category: Viable but non-culturable state]]
 
[[Category: Vibrio parahaemolyticus]]
[[Category: Vibrio parahaemolyticus]]
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[[Category: Ygjd]]
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[[Category: Aydin I]]
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[[Category: Yjee]]
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[[Category: Roujeinikova A]]

Current revision

Crystal structure of Vibrio parahaemolyticus YeaZ

PDB ID 3r6m

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