1mdf

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1mdf" size="450" color="white" frame="true" align="right" spinBox="true" caption="1mdf, resolution 2.50&Aring;" /> '''CRYSTAL STRUCTURE OF...)
Current revision (07:43, 14 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1mdf.gif|left|200px]]<br /><applet load="1mdf" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1mdf, resolution 2.50&Aring;" />
 
-
'''CRYSTAL STRUCTURE OF DhbE IN ABSENCE OF SUBSTRATE'''<br />
 
-
==Overview==
+
==CRYSTAL STRUCTURE OF DhbE IN ABSENCE OF SUBSTRATE==
-
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='1mdf' size='340' side='right'caption='[[1mdf]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<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>
-
1MDF 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 SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1MDF 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]] 2.5&#8491;</td></tr>
-
 
+
<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>
-
==Reference==
+
<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>
-
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/1mdf_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=1mdf ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
-
[[Category: Single protein]]
+
[[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: 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 21:20:42 2007''
+

Current revision

CRYSTAL STRUCTURE OF DhbE IN ABSENCE OF SUBSTRATE

PDB ID 1mdf

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1mdf"
Personal tools