3mdd: Difference between revisions

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New page: left|200px<br /><applet load="3mdd" size="450" color="white" frame="true" align="right" spinBox="true" caption="3mdd, resolution 2.4Å" /> '''CRYSTAL STRUCTURES OF...
 
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[[Image:3mdd.jpg|left|200px]]<br /><applet load="3mdd" size="450" color="white" frame="true" align="right" spinBox="true"
caption="3mdd, resolution 2.4&Aring;" />
'''CRYSTAL STRUCTURES OF MEDIUM CHAIN ACYL-COA DEHYDROGENASE FROM PIG LIVER MITOCHONDRIA WITH AND WITHOUT SUBSTRATE'''<br />


==Overview==
==CRYSTAL STRUCTURES OF MEDIUM CHAIN ACYL-COA DEHYDROGENASE FROM PIG LIVER MITOCHONDRIA WITH AND WITHOUT SUBSTRATE==
The three-dimensional structure of medium-chain acyl-CoA dehydrogenase, from pig mitochondria in the native form and that of a complex of the, enzyme and a substrate (product) have been solved and refined by x-ray, crystallographic methods at 2.4-A resolution to R factors of 0.172 and, 0.173, respectively. The overall polypeptide folding and the quaternary, structure of the tetramer are essentially unchanged upon binding of the, ligand, octanoyl (octenoyl)-CoA. The ligand binds to the enzyme at the, rectus (re) face of the FAD in the crevice between the two alpha-helix, domains and the beta-sheet domain of the enzyme. The fatty acyl chain of, the thioester substrate is buried inside of the polypeptide and the 3'-AMP, moiety is close to the surface of the tetrameric enzyme molecule. The, alkyl chain displaces the tightly bound water molecules found in the, native enzyme and the carbonyl oxygen of the thioester interacts with the, ribityl 2'-hydroxyl group of the FAD and the main-chain carbonyl oxygen of, Glu-376. The C alpha--C beta of the fatty acyl moiety lies between the, flavin and the gamma-carboxylate of Glu-376, supporting the role of, Glu-376 as the base that abstracts the alpha proton in the alpha--beta, dehydrogenation reaction catalyzed by the enzyme. Trp-166 and Met-165 are, located at the sinister (si) side of the flavin ring at the surface of the, enzyme, suggesting that they might be involved in the interactions with, electron transferring flavoprotein. Lys-304, the prevalent mutation site, found in patients with medium-chain acyl-CoA dehydrogenase deficiency, is, located approximately 20 A away from the active site of the enzyme.
<StructureSection load='3mdd' size='340' side='right'caption='[[3mdd]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3mdd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MDD FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
<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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3mdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mdd OCA], [https://pdbe.org/3mdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mdd RCSB], [https://www.ebi.ac.uk/pdbsum/3mdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mdd ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ACADM_PIG ACADM_PIG] This enzyme is specific for acyl chain lengths of 4 to 16.
== 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/3mdd_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=3mdd ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
3MDD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with FAD as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Acyl-CoA_dehydrogenase Acyl-CoA dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.99.3 1.3.99.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=3MDD OCA].
*[[Acyl-CoA dehydrogenase 3D structures|Acyl-CoA dehydrogenase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate., Kim JJ, Wang M, Paschke R, Proc Natl Acad Sci U S A. 1993 Aug 15;90(16):7523-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8356049 8356049]
[[Category: Large Structures]]
[[Category: Acyl-CoA dehydrogenase]]
[[Category: Single protein]]
[[Category: Sus scrofa]]
[[Category: Sus scrofa]]
[[Category: Kim, J.J.P.]]
[[Category: Kim J-JP]]
[[Category: Paschke, R.]]
[[Category: Paschke R]]
[[Category: Wang, M.]]
[[Category: Wang M]]
[[Category: FAD]]
[[Category: oxidoreductase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:51:43 2007''

Latest revision as of 13:24, 21 February 2024

CRYSTAL STRUCTURES OF MEDIUM CHAIN ACYL-COA DEHYDROGENASE FROM PIG LIVER MITOCHONDRIA WITH AND WITHOUT SUBSTRATECRYSTAL STRUCTURES OF MEDIUM CHAIN ACYL-COA DEHYDROGENASE FROM PIG LIVER MITOCHONDRIA WITH AND WITHOUT SUBSTRATE

Structural highlights

3mdd is a 2 chain structure with sequence from Sus scrofa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ACADM_PIG This enzyme is specific for acyl chain lengths of 4 to 16.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

3mdd, resolution 2.40Å

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