2gel

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[[Image:2gel.gif|left|200px]]
 
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==2.05A crystal structure of Salmonella typhimurium YeaZ, form B==
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The line below this paragraph, containing "STRUCTURE_2gel", creates the "Structure Box" on the page.
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<StructureSection load='2gel' size='340' side='right'caption='[[2gel]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2gel]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GEL FirstGlance]. <br>
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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]] 2.05&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gel OCA], [https://pdbe.org/2gel PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gel RCSB], [https://www.ebi.ac.uk/pdbsum/2gel PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gel ProSAT]</span></td></tr>
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{{STRUCTURE_2gel| PDB=2gel | SCENE= }}
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</table>
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== Function ==
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'''2.05A crystal structure of Salmonella typhimurium YeaZ, form B'''
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[https://www.uniprot.org/uniprot/TSAB_SALTY TSAB_SALTY] 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). Neither binds polyphosphates nor a wide range of nucleotides on its own. Does not show O-sialoglycoprotein endopeptidase activity. Has been identified as the first Gram-negative bacterial RPF (Resuscitation-Promoting Factor) capable of reviving VNC (viable but non-culturable) cells when added externally, but the million-fold lower activity as compared to Gram-positive bacterial RPFs may indicate a lack of physiological relevance.<ref>PMID:16213054</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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==Overview==
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Check<jmol>
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The Salmonella typhimurium "yeaZ" gene (StyeaZ) encodes an essential protein of unknown function (StYeaZ), which has previously been annotated as a putative homolog of the Pasteurella haemolytica M22 O-sialoglycoprotein endopeptidase Gcp. YeaZ has also recently been reported as the first example of an RPF from a gram-negative bacterial species. To further characterize the properties of StYeaZ and the widely occurring MK-M22 family, we describe the purification, biochemical analysis, crystallization, and structure determination of StYeaZ. The crystal structure of StYeaZ reveals a classic two-lobed actin-like fold with structural features consistent with nucleotide binding. However, microcalorimetry experiments indicated that StYeaZ neither binds polyphosphates nor a wide range of nucleotides. Additionally, biochemical assays show that YeaZ is not an active O-sialoglycoprotein endopeptidase, consistent with the lack of the critical zinc binding motif. We present a detailed comparison of YeaZ with available structural homologs, the first reported structural analysis of an MK-M22 family member. The analysis indicates that StYeaZ has an unusual orientation of the A and B lobes which may require substantial relative movement or interaction with a partner protein in order to bind ligands. Comparison of the fold of YeaZ with that of a known RPF domain from a gram-positive species shows significant structural differences and therefore potentially distinctive RPF mechanisms for these two bacterial classes.
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ge/2gel_consurf.spt"</scriptWhenChecked>
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==About this Structure==
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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2GEL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEL OCA].
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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==Reference==
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2gel ConSurf].
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Structural characterization of Salmonella typhimurium YeaZ, an M22 O-sialoglycoprotein endopeptidase homolog., Nichols CE, Johnson C, Lockyer M, Charles IG, Lamb HK, Hawkins AR, Stammers DK, Proteins. 2006 Jul 1;64(1):111-23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16617437 16617437]
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<div style="clear:both"></div>
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[[Category: Salmonella typhimurium]]
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== References ==
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[[Category: Single protein]]
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<references/>
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[[Category: Nichols, C E.]]
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__TOC__
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[[Category: Stammers, D K.]]
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</StructureSection>
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[[Category: Actin-like-fold]]
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[[Category: Large Structures]]
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[[Category: Glycoprotease]]
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[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
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[[Category: M22]]
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[[Category: Nichols CE]]
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[[Category: Rpf]]
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[[Category: Stammers DK]]
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[[Category: Yeaz]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 05:00:53 2008''
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Current revision

2.05A crystal structure of Salmonella typhimurium YeaZ, form B

PDB ID 2gel

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