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1wkq

From Proteopedia

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[[Image:1wkq.gif|left|200px]]<br /><applet load="1wkq" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1wkq, resolution 1.17&Aring;" />
 
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'''Crystal Structure of Bacillus subtilis Guanine Deaminase. The first domain-swapped structure in the cytidine deaminase superfamily'''<br />
 
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==Overview==
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==Crystal Structure of Bacillus subtilis Guanine Deaminase. The first domain-swapped structure in the cytidine deaminase superfamily==
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Guanine deaminase, a key enzyme in the nucleotide metabolism, catalyzes the hydrolytic deamination of guanine into xanthine. The crystal structure of the 156-residue guanine deaminase from Bacillus subtilis has been solved at 1.17-A resolution. Unexpectedly, the C-terminal segment is swapped to form an intersubunit active site and an intertwined dimer with an extensive interface of 3900 A(2) per monomer. The essential zinc ion is ligated by a water molecule together with His(53), Cys(83), and Cys(86). A transition state analog was modeled into the active site cavity based on the tightly bound imidazole and water molecules, allowing identification of the conserved deamination mechanism and specific substrate recognition by Asp(114) and Tyr(156'). The closed conformation also reveals that substrate binding seals the active site entrance, which is controlled by the C-terminal tail. Therefore, the domain swapping has not only facilitated the dimerization but has also ensured specific substrate recognition. Finally, a detailed structural comparison of the cytidine deaminase superfamily illustrates the functional versatility of the divergent active sites found in the guanine, cytosine, and cytidine deaminases and suggests putative specific substrate-interacting residues for other members such as dCMP deaminases.
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<StructureSection load='1wkq' size='340' side='right'caption='[[1wkq]], [[Resolution|resolution]] 1.17&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1wkq]] is a 2 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=1WKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WKQ 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]] 1.17&#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=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1wkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkq OCA], [https://pdbe.org/1wkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wkq RCSB], [https://www.ebi.ac.uk/pdbsum/1wkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wkq ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/GUAD_BACSU GUAD_BACSU] Catalyzes the hydrolytic deamination of guanine, producing xanthine and ammonia.
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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/wk/1wkq_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=1wkq ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1WKQ 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 <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=IMD:'>IMD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Guanine_deaminase Guanine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.3 3.5.4.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKQ OCA].
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*[[Deaminase 3D structures|Deaminase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structure of Bacillus subtilis guanine deaminase: the first domain-swapped structure in the cytidine deaminase superfamily., Liaw SH, Chang YJ, Lai CT, Chang HC, Chang GG, J Biol Chem. 2004 Aug 20;279(34):35479-85. Epub 2004 Jun 4. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15180998 15180998]
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[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
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[[Category: Guanine deaminase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Chang YJ]]
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[[Category: Chang, Y J.]]
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[[Category: Lai CT]]
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[[Category: Lai, C T.]]
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[[Category: Liaw SH]]
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[[Category: Liaw, S H.]]
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[[Category: IMD]]
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[[Category: ZN]]
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[[Category: domain swap]]
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[[Category: guanine deaminase]]
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[[Category: structural plasticity]]
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[[Category: substrate specificity]]
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[[Category: the cytidine deaminase superfamily]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:45:23 2008''
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Current revision

Crystal Structure of Bacillus subtilis Guanine Deaminase. The first domain-swapped structure in the cytidine deaminase superfamily

PDB ID 1wkq

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