1u8v: Difference between revisions

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{{Seed}}
[[Image:1u8v.png|left|200px]]


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==Crystal Structure of 4-Hydroxybutyryl-CoA Dehydratase from Clostridium aminobutyricum: Radical catalysis involving a [4Fe-4S] cluster and flavin==
The line below this paragraph, containing "STRUCTURE_1u8v", creates the "Structure Box" on the page.
<StructureSection load='1u8v' size='340' side='right'caption='[[1u8v]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1u8v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_aminobutyricum Clostridium aminobutyricum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U8V FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
{{STRUCTURE_1u8v|  PDB=1u8v  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1u8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u8v OCA], [https://pdbe.org/1u8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u8v RCSB], [https://www.ebi.ac.uk/pdbsum/1u8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u8v ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/HDVD_CLOAM HDVD_CLOAM] Catalyzes the reversible conversion of 4-hydroxybutyryl-CoA to crotonyl-CoA. The mechanism of the reaction seems to go through three steps: (1) the FAD-dependent oxidation of 4-hydroxybutyryl-CoA to 4-hydroxycrotonyl-CoA; (2) the hydroxyl group is substituted by a hydride derived from the now reduced FAD in an SN2' reaction leading to vinylacetyl-CoA; (3) isomerization to yield crotonyl-CoA.
== 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/u8/1u8v_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1u8v ConSurf].
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== Publication Abstract from PubMed ==
Dehydratases catalyze the breakage of a carbon-oxygen bond leading to unsaturated products via the elimination of water. The 1.6-A resolution crystal structure of 4-hydroxybutyryl-CoA dehydratase from the gamma-aminobutyrate-fermenting Clostridium aminobutyricum represents a new class of dehydratases with an unprecedented active site architecture. A [4Fe-4S](2+) cluster, coordinated by three cysteine and one histidine residues, is located 7 A from the Re-side of a flavin adenine dinucleotide (FAD) moiety. The structure provides insight into the function of these ubiquitous prosthetic groups in the chemically nonfacile, radical-mediated dehydration of 4-hydroxybutyryl-CoA. The substrate can be bound between the [4Fe-4S](2+) cluster and the FAD with both cofactors contributing to its radical activation and catalytic conversion. Our results raise interesting questions regarding the mechanism of acyl-CoA dehydrogenases, which are involved in fatty acid oxidation, and address the divergent evolution of the ancestral common gene.


===Crystal Structure of 4-Hydroxybutyryl-CoA Dehydratase from Clostridium aminobutyricum: Radical catalysis involving a [4Fe-4S] cluster and flavin===
Crystal structure of 4-hydroxybutyryl-CoA dehydratase: radical catalysis involving a [4Fe-4S] cluster and flavin.,Martins BM, Dobbek H, Cinkaya I, Buckel W, Messerschmidt A Proc Natl Acad Sci U S A. 2004 Nov 2;101(44):15645-9. Epub 2004 Oct 20. PMID:15496473<ref>PMID:15496473</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 1u8v" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 15496473 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_15496473}}
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</StructureSection>
==About this Structure==
1U8V is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Clostridium_aminobutyricum Clostridium aminobutyricum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U8V OCA].
 
==Reference==
<ref group="xtra">PMID:15496473</ref><references group="xtra"/>
[[Category: Clostridium aminobutyricum]]
[[Category: Clostridium aminobutyricum]]
[[Category: Buckel, W.]]
[[Category: Large Structures]]
[[Category: Cinkaya, I.]]
[[Category: Buckel W]]
[[Category: Dobbek, H.]]
[[Category: Cinkaya I]]
[[Category: Martins, B M.]]
[[Category: Dobbek H]]
[[Category: Messerschmidt, A.]]
[[Category: Martins BM]]
[[Category: Alfa-helix]]
[[Category: Messerschmidt A]]
[[Category: Beta-strand]]
[[Category: Isomerase]]
[[Category: Lyase]]
 
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Retrieved from "https://proteopedia.org/1u8v"