1mdf

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[[Image:1mdf.gif|left|200px]]
 
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{{Structure
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==CRYSTAL STRUCTURE OF DhbE IN ABSENCE OF SUBSTRATE==
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|PDB= 1mdf |SIZE=350|CAPTION= <scene name='initialview01'>1mdf</scene>, resolution 2.50&Aring;
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<StructureSection load='1mdf' size='340' side='right'caption='[[1mdf]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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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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|ACTIVITY=
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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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|GENE=
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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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|DOMAIN=
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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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|RELATEDENTRY=[[1amu|1AMU]], [[1md9|1MD9]], [[1mdb|1MDB]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1mdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mdf OCA], [http://www.ebi.ac.uk/pdbsum/1mdf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1mdf RCSB]</span>
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== Function ==
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}}
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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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'''CRYSTAL STRUCTURE OF DhbE IN ABSENCE OF SUBSTRATE'''
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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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==Overview==
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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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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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<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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==About this Structure==
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</jmolCheckbox>
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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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</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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==Reference==
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__TOC__
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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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</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 Sun Mar 30 22:14:40 2008''
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Current revision

CRYSTAL STRUCTURE OF DhbE IN ABSENCE OF SUBSTRATE

PDB ID 1mdf

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