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1qd9

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[[Image:1qd9.gif|left|200px]]
 
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==Bacillus subtilis YABJ==
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The line below this paragraph, containing "STRUCTURE_1qd9", creates the "Structure Box" on the page.
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<StructureSection load='1qd9' size='340' side='right'caption='[[1qd9]], [[Resolution|resolution]] 1.70&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'>[[1qd9]] is a 3 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=1QD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QD9 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.7&#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=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=EMC:ETHYL+MERCURY+ION'>EMC</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
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{{STRUCTURE_1qd9| PDB=1qd9 | SCENE= }}
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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=1qd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qd9 OCA], [https://pdbe.org/1qd9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qd9 RCSB], [https://www.ebi.ac.uk/pdbsum/1qd9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qd9 ProSAT]</span></td></tr>
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</table>
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'''Bacillus subtilis YABJ'''
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== Function ==
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[https://www.uniprot.org/uniprot/RIDA_BACSU RIDA_BACSU] Accelerates the release of ammonia from reactive enamine/imine intermediates of the PLP-dependent threonine dehydratase (IlvA) in the low water environment of the cell. It catalyzes the deamination of enamine/imine intermediates to yield 2-ketobutyrate and ammonia. It is required for the detoxification of reactive intermediates of IlvA due to their highly nucleophilic abilities. Involved in the isoleucine biosynthesis. May have a role in the purine metabolism.<ref>PMID:22094463</ref>
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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The yabJ gene in Bacillus subtilis is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The molecular mechanism of YabJ is unknown. YabJ is a member of a large, widely distributed family of proteins of unknown biochemical function. The 1.7-A crystal structure of YabJ reveals a trimeric organization with extensive buried hydrophobic surface and an internal water-filled cavity. The most important finding in the structure is a deep, narrow cleft between subunits lined with nine side chains that are invariant among the 25 most similar homologs. This conserved site is proposed to be a binding or catalytic site for a ligand or substrate that is common to YabJ and other members of the YER057c/YjgF/UK114 family of proteins.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qd/1qd9_consurf.spt"</scriptWhenChecked>
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1QD9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QD9 OCA].
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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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==Reference==
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</jmolCheckbox>
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Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family., Sinha S, Rappu P, Lange SC, Mantsala P, Zalkin H, Smith JL, Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13074-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10557275 10557275]
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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=1qd9 ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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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: Lange, S C.]]
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[[Category: Lange SC]]
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[[Category: Mantsala, P.]]
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[[Category: Mantsala P]]
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[[Category: Rappu, P.]]
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[[Category: Rappu P]]
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[[Category: Sinha, S.]]
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[[Category: Sinha S]]
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[[Category: Smith, J L.]]
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[[Category: Smith JL]]
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[[Category: Zalkin, H.]]
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[[Category: Zalkin H]]
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[[Category: Gene regulation]]
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[[Category: Perchloric acid soluble protein]]
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[[Category: Purine regulation]]
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[[Category: Yjgf/yer057c family]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 06:09:10 2008''
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Current revision

Bacillus subtilis YABJ

PDB ID 1qd9

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