1mdb

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:43, 14 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1mdb.gif|left|200px]]
 
-
{{Structure
+
==CRYSTAL STRUCTURE OF DhbE IN COMPLEX WITH DHB-ADENYLATE==
-
|PDB= 1mdb |SIZE=350|CAPTION= <scene name='initialview01'>1mdb</scene>, resolution 2.15&Aring;
+
<StructureSection load='1mdb' size='340' side='right'caption='[[1mdb]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <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>
+
<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>
-
|ACTIVITY=
+
</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>
-
|GENE=
+
<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>
-
|DOMAIN=
+
<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>
-
|RELATEDENTRY=[[1amu|1AMU]], [[1md9|1MD9]], [[1mdf|1MDF]]
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1mdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mdb OCA], [http://www.ebi.ac.uk/pdbsum/1mdb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1mdb RCSB]</span>
+
== 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 ==
-
'''CRYSTAL STRUCTURE OF DhbE IN COMPLEX WITH DHB-ADENYLATE'''
+
[[Image:Consurf_key_small.gif|200px|right]]
-
 
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==Overview==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/md/1mdb_consurf.spt"</scriptWhenChecked>
-
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.
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==About this Structure==
+
</jmolCheckbox>
-
1MDB is a [[Protein complex]] structure of sequences 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=1MDB OCA].
+
</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>
-
==Reference==
+
__TOC__
-
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]
+
</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: adenylation domain]]
+
-
[[Category: antibiotic biosynthesis]]
+
-
[[Category: ligase]]
+
-
[[Category: peptide synthetase]]
+
-
[[Category: siderophore formation]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:14:40 2008''
+

Current revision

CRYSTAL STRUCTURE OF DhbE IN COMPLEX WITH DHB-ADENYLATE

PDB ID 1mdb

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/1mdb"
Personal tools