1t9h

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(New page: 200px<br /><applet load="1t9h" size="450" color="white" frame="true" align="right" spinBox="true" caption="1t9h, resolution 1.60&Aring;" /> '''The crystal structur...)
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[[Image:1t9h.gif|left|200px]]<br /><applet load="1t9h" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1t9h, resolution 1.60&Aring;" />
 
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'''The crystal structure of YloQ, a circularly permuted GTPase.'''<br />
 
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==Overview==
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==The crystal structure of YloQ, a circularly permuted GTPase.==
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yloQ is one of 11 essential genes in Bacillus subtilis with unknown roles, in the physiology of the cell. It encodes a polypeptide of 298 residues, with motifs characteristic of GTPases. As a contribution to elucidating, its indispensable cellular function, we have solved the crystal structure, of YloQ to 1.6 A spacing, revealing a three-domain organisation. At the, heart of the molecule is the putative GTPase domain, which exhibits a, classical alpha/beta nucleotide-binding fold with a topology very similar, to that of Ras and Era. However, as anticipated from the order in which, the conserved G protein motifs appear in the sequence, the GTPase domain, fold in YloQ is circularly permuted with respect to the classical GTPases., The nucleotide-binding pocket in YloQ is unoccupied, and analysis of the, phosphate-binding (P) loop indicates that conformational changes in this, region would be needed to accommodate GTP. The GTPase domain is flanked at, its N terminus by a beta-barrel domain with an, oligonucleotide/oligosaccharide-binding (OB) fold, and at its C terminus, by an alpha-helical domain containing a coordinated zinc ion. This, combination of protein modules is unique to YloQ and its orthologues., Sequence comparisons reveal a clustering of conserved basic and aromatic, residues on one face of the OB domain, perhaps pointing to a role for YloQ, in nucleic acid binding. The zinc ion in the alpha-helical domain is, coordinated by three cysteine residues and a histidine residue in a novel, ligand organisation. The juxtaposition of the switch I and switch II, regions of the G domain and the OB and zinc-binding domains suggests that, chemical events at the GTPase active site may be transduced into relative, movements of these domains. The pattern of conserved residues and, electrostatic surface potential calculations suggest that the OB and/or, Zn-binding domains participate in nucleic acid binding consistent with a, possible role for YloQ at some stage during mRNA translation.
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<StructureSection load='1t9h' size='340' side='right'caption='[[1t9h]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1t9h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T9H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T9H FirstGlance]. <br>
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1T9H is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with IUM, ZN, CA and ACT as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1T9H OCA].
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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]] 1.6&#8491;</td></tr>
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<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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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==Reference==
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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=1t9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t9h OCA], [https://pdbe.org/1t9h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t9h RCSB], [https://www.ebi.ac.uk/pdbsum/1t9h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t9h ProSAT]</span></td></tr>
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The crystal structure of YloQ, a circularly permuted GTPase essential for Bacillus subtilis viability., Levdikov VM, Blagova EV, Brannigan JA, Cladiere L, Antson AA, Isupov MN, Seror SJ, Wilkinson AJ, J Mol Biol. 2004 Jul 16;340(4):767-82. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15223319 15223319]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RSGA_BACSU RSGA_BACSU] Depletion of yloQ results in sensitization towards protein synthesis inhibitors that block the peptide channel or peptidyl transferase center on the ribosome, implying that YloQ functions in conjunction with the ribosome in vivo. Decreasing levels of YloQ lead to an increase in unassembled 30S and 50S subunit and a decrease in the assembled 70S ribosome. May play a role in 30S ribosomal subunit biogenesis. Unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover (By similarity). Dispensible for viability, but important for overall fitness.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t9/1t9h_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1t9h ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Antson, A.A.]]
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[[Category: Antson AA]]
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[[Category: Blagova, E.V.]]
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[[Category: Blagova EV]]
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[[Category: Brannigan, J.A.]]
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[[Category: Brannigan JA]]
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[[Category: Cladiere, L.]]
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[[Category: Cladiere L]]
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[[Category: Isupov, M.N.]]
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[[Category: Isupov MN]]
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[[Category: Levdikov, V.M.]]
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[[Category: Levdikov VM]]
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[[Category: Seror, S.J.]]
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[[Category: Seror SJ]]
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[[Category: Wilkinson, A.J.]]
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[[Category: Wilkinson AJ]]
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[[Category: ACT]]
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[[Category: CA]]
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[[Category: IUM]]
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[[Category: ZN]]
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[[Category: c-terminal zinc-binding domain]]
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[[Category: central gtp binding domain]]
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[[Category: n-terminal beta-barrel domain with oligonucleotide binding fold]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 03:05:58 2007''
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Current revision

The crystal structure of YloQ, a circularly permuted GTPase.

PDB ID 1t9h

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