1mdf

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[[Image:1mdf.gif|left|200px]]
 
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==CRYSTAL STRUCTURE OF DhbE IN ABSENCE OF SUBSTRATE==
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The line below this paragraph, containing "STRUCTURE_1mdf", creates the "Structure Box" on the page.
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<StructureSection load='1mdf' size='340' side='right'caption='[[1mdf]], [[Resolution|resolution]] 2.50&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'>[[1mdf]] 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=1MDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MDF 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]] 2.5&#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=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_1mdf| PDB=1mdf | 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=1mdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mdf OCA], [https://pdbe.org/1mdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mdf RCSB], [https://www.ebi.ac.uk/pdbsum/1mdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mdf ProSAT]</span></td></tr>
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</table>
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'''CRYSTAL STRUCTURE OF DhbE IN ABSENCE OF SUBSTRATE'''
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== Function ==
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[https://www.uniprot.org/uniprot/DHBE_BACSU DHBE_BACSU] Activation of the carboxylate group of 2,3-dihydroxy-benzoate (DHB), via ATP-dependent PPi exchange reactions, to the acyladenylate.
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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 synthesis of the catecholic siderophore bacillibactin is accomplished by the nonribosomal peptide synthetase (NRPS) encoded by the dhb operon. DhbE is responsible for the initial step in bacillibactin synthesis, the activation of the aryl acid 2,3-dihydroxybenzoate (DHB). The stand-alone adenylation (A) domain DhbE, the structure of which is presented here, exhibits greatest homology to other NRPS A-domains, acyl-CoA ligases and luciferases. It's structure is solved in three different states, without the ligands ATP and DHB (native state), with the product DHB-AMP (adenylate state) and with the hydrolyzed product AMP and DHB (hydrolyzed state). The 59.9-kDa protein folds into two domains, with the active site at the interface between them. In contrast to previous proposals of a major reorientation of the large and small domains on substrate binding, we observe only local structural rearrangements. The structure of the phosphate binding loop could be determined, a motif common to many adenylate-forming enzymes, as well as with bound DHB-adenylate and the hydrolyzed product DHB*AMP. Based on the structure and amino acid sequence alignments, an adapted specificity conferring code for aryl acid activating domains is proposed, allowing assignment of substrate specificity to gene products of previously unknown function.
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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/md/1mdf_consurf.spt"</scriptWhenChecked>
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1MDF 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=1MDF 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 DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases., May JJ, Kessler N, Marahiel MA, Stubbs MT, Proc Natl Acad Sci U S A. 2002 Sep 17;99(19):12120-5. Epub 2002 Sep 9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12221282 12221282]
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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=1mdf 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: Kessler, N.]]
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[[Category: Kessler N]]
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[[Category: Marahiel, M A.]]
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[[Category: Marahiel MA]]
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[[Category: May, J J.]]
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[[Category: May JJ]]
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[[Category: Stubbs, M T.]]
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[[Category: Stubbs MT]]
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[[Category: Adenylation domain]]
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[[Category: Antibiotic biosynthesis]]
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[[Category: Ligase]]
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[[Category: Peptide synthetase]]
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[[Category: Siderophore formation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 00:54:39 2008''
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Current revision

CRYSTAL STRUCTURE OF DhbE IN ABSENCE OF SUBSTRATE

PDB ID 1mdf

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