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New page: left|200px<br /><applet load="1mdb" size="450" color="white" frame="true" align="right" spinBox="true" caption="1mdb, resolution 2.15Å" /> '''CRYSTAL STRUCTURE OF...
 
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[[Image:1mdb.gif|left|200px]]<br /><applet load="1mdb" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1mdb, resolution 2.15&Aring;" />
'''CRYSTAL STRUCTURE OF DhbE IN COMPLEX WITH DHB-ADENYLATE'''<br />


==Overview==
==CRYSTAL STRUCTURE OF DhbE IN COMPLEX WITH DHB-ADENYLATE==
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.
<StructureSection load='1mdb' size='340' side='right'caption='[[1mdb]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1mdb]] 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=1MDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MDB FirstGlance]. <br>
1MDB is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with SO4, AMP and DBH as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1MDB OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=DBH:2,3-DIHYDROXY-BENZOIC+ACID'>DBH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mdb OCA], [https://pdbe.org/1mdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mdb RCSB], [https://www.ebi.ac.uk/pdbsum/1mdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mdb ProSAT]</span></td></tr>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12221282 12221282]
</table>
== Function ==
[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.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/md/1mdb_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1mdb ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Kessler, N.]]
[[Category: Kessler N]]
[[Category: Marahiel, M.A.]]
[[Category: Marahiel MA]]
[[Category: May, J.J.]]
[[Category: May JJ]]
[[Category: Stubbs, M.T.]]
[[Category: Stubbs MT]]
[[Category: AMP]]
[[Category: DBH]]
[[Category: SO4]]
[[Category: adenylation domain]]
[[Category: antibiotic biosynthesis]]
[[Category: ligase]]
[[Category: peptide synthetase]]
[[Category: siderophore formation]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:20:35 2007''

Latest revision as of 07:43, 14 February 2024

CRYSTAL STRUCTURE OF DhbE IN COMPLEX WITH DHB-ADENYLATE

1mdb, resolution 2.15Å

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