2jif: Difference between revisions

Latest revision as of 14:50, 13 December 2023

Structure of human short-branched chain acyl-CoA dehydrogenase (ACADSB)

Structural highlights

2jif is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	CL, COS, EDO, FAD
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

ACDSB_HUMAN 2-methylbutyryl-CoA dehydrogenase deficiency. The disease is caused by variants affecting the gene represented in this entry.

Function

ACDSB_HUMAN Short and branched chain specific acyl-CoA dehydrogenase that catalyzes the removal of one hydrogen from C-2 and C-3 of the fatty acyl-CoA thioester, resulting in the formation of trans-2-enoyl-CoA (PubMed:7698750, PubMed:11013134, PubMed:21430231, PubMed:10832746). Among the different mitochondrial acyl-CoA dehydrogenases, acts specifically on short and branched chain acyl-CoA derivatives such as (S)-2-methylbutyryl-CoA as well as short straight chain acyl-CoAs such as butyryl-CoA (PubMed:7698750, PubMed:11013134, PubMed:21430231, PubMed:10832746). Plays an important role in the metabolism of L-isoleucine by catalyzing the dehydrogenation of 2-methylbutyryl-CoA, one of the steps of the L-isoleucine catabolic pathway (PubMed:11013134, PubMed:10832746). Can also act on valproyl-CoA, a metabolite of valproic acid, an antiepileptic drug (PubMed:8660691).^[1] ^[2] ^[3] ^[4] ^[5]

Evolutionary Conservation

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

References

↑ Gibson KM, Burlingame TG, Hogema B, Jakobs C, Schutgens RB, Millington D, Roe CR, Roe DS, Sweetman L, Steiner RD, Linck L, Pohowalla P, Sacks M, Kiss D, Rinaldo P, Vockley J. 2-Methylbutyryl-coenzyme A dehydrogenase deficiency: a new inborn error of L-isoleucine metabolism. Pediatr Res. 2000 Jun;47(6):830-3. PMID:10832746 doi:10.1203/00006450-200006000-00025
↑ Andresen BS, Christensen E, Corydon TJ, Bross P, Pilgaard B, Wanders RJ, Ruiter JP, Simonsen H, Winter V, Knudsen I, Schroeder LD, Gregersen N, Skovby F. Isolated 2-methylbutyrylglycinuria caused by short/branched-chain acyl-CoA dehydrogenase deficiency: identification of a new enzyme defect, resolution of its molecular basis, and evidence for distinct acyl-CoA dehydrogenases in isoleucine and valine metabolism. Am J Hum Genet. 2000 Nov;67(5):1095-103. Epub 2000 Sep 29. PMID:11013134 doi:10.1086/303105
↑ Luís PB, Ruiter JP, Ijlst L, Tavares de Almeida I, Duran M, Mohsen AW, Vockley J, Wanders RJ, Silva MF. Role of isovaleryl-CoA dehydrogenase and short branched-chain acyl-CoA dehydrogenase in the metabolism of valproic acid: implications for the branched-chain amino acid oxidation pathway. Drug Metab Dispos. 2011 Jul;39(7):1155-60. PMID:21430231 doi:10.1124/dmd.110.037606
↑ Rozen R, Vockley J, Zhou L, Milos R, Willard J, Fu K, Vicanek C, Low-Nang L, Torban E, Fournier B. Isolation and expression of a cDNA encoding the precursor for a novel member (ACADSB) of the acyl-CoA dehydrogenase gene family. Genomics. 1994 Nov 15;24(2):280-7. PMID:7698750 doi:10.1006/geno.1994.1617
↑ Willard J, Vicanek C, Battaile KP, Van Veldhoven PP, Fauq AH, Rozen R, Vockley J. Cloning of a cDNA for short/branched chain acyl-Coenzyme A dehydrogenase from rat and characterization of its tissue expression and substrate specificity. Arch Biochem Biophys. 1996 Jul 1;331(1):127-33. PMID:8660691 doi:10.1006/abbi.1996.0290

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Gibson KM, Burlingame TG, Hogema B, Jakobs C, Schutgens RB, Millington D, Roe CR, Roe DS, Sweetman L, Steiner RD, Linck L, Pohowalla P, Sacks M, Kiss D, Rinaldo P, Vockley J. 2-Methylbutyryl-coenzyme A dehydrogenase deficiency: a new inborn error of L-isoleucine metabolism. Pediatr Res. 2000 Jun;47(6):830-3. PMID:10832746 doi:10.1203/00006450-200006000-00025

[2] Andresen BS, Christensen E, Corydon TJ, Bross P, Pilgaard B, Wanders RJ, Ruiter JP, Simonsen H, Winter V, Knudsen I, Schroeder LD, Gregersen N, Skovby F. Isolated 2-methylbutyrylglycinuria caused by short/branched-chain acyl-CoA dehydrogenase deficiency: identification of a new enzyme defect, resolution of its molecular basis, and evidence for distinct acyl-CoA dehydrogenases in isoleucine and valine metabolism. Am J Hum Genet. 2000 Nov;67(5):1095-103. Epub 2000 Sep 29. PMID:11013134 doi:10.1086/303105

[3] Luís PB, Ruiter JP, Ijlst L, Tavares de Almeida I, Duran M, Mohsen AW, Vockley J, Wanders RJ, Silva MF. Role of isovaleryl-CoA dehydrogenase and short branched-chain acyl-CoA dehydrogenase in the metabolism of valproic acid: implications for the branched-chain amino acid oxidation pathway. Drug Metab Dispos. 2011 Jul;39(7):1155-60. PMID:21430231 doi:10.1124/dmd.110.037606

[4] Rozen R, Vockley J, Zhou L, Milos R, Willard J, Fu K, Vicanek C, Low-Nang L, Torban E, Fournier B. Isolation and expression of a cDNA encoding the precursor for a novel member (ACADSB) of the acyl-CoA dehydrogenase gene family. Genomics. 1994 Nov 15;24(2):280-7. PMID:7698750 doi:10.1006/geno.1994.1617

[5] Willard J, Vicanek C, Battaile KP, Van Veldhoven PP, Fauq AH, Rozen R, Vockley J. Cloning of a cDNA for short/branched chain acyl-Coenzyme A dehydrogenase from rat and characterization of its tissue expression and substrate specificity. Arch Biochem Biophys. 1996 Jul 1;331(1):127-33. PMID:8660691 doi:10.1006/abbi.1996.0290

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[2]

[3]

[4]

[5]

@@ Line 1: / Line 1: @@
-[[Image:2jif.gif|left|200px]]<br />
-<applet load="2jif" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2jif, resolution 2.00&Aring;" />
-'''STRUCTURE OF HUMAN SHORT-BRANCHED CHAIN ACYL-COA DEHYDROGENASE (ACADSB)'''<br />
-==About this Structure==
+==Structure of human short-branched chain acyl-CoA dehydrogenase (ACADSB)==
-JIF is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]] with CL, FAD, COS and EDO as [[http://en.wikipedia.org/wiki/ligands ligands]]. Structure known Active Site: AC1. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2JIF OCA]].
+<StructureSection load='2jif' size='340' side='right'caption='[[2jif]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2jif]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JIF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JIF 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=COS:COENZYME+A+PERSULFIDE'>COS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <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=2jif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jif OCA], [https://pdbe.org/2jif PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jif RCSB], [https://www.ebi.ac.uk/pdbsum/2jif PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jif ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/ACDSB_HUMAN ACDSB_HUMAN] 2-methylbutyryl-CoA dehydrogenase deficiency. The disease is caused by variants affecting the gene represented in this entry.
+== Function ==
+[https://www.uniprot.org/uniprot/ACDSB_HUMAN ACDSB_HUMAN] Short and branched chain specific acyl-CoA dehydrogenase that catalyzes the removal of one hydrogen from C-2 and C-3 of the fatty acyl-CoA thioester, resulting in the formation of trans-2-enoyl-CoA (PubMed:7698750, PubMed:11013134, PubMed:21430231, PubMed:10832746). Among the different mitochondrial acyl-CoA dehydrogenases, acts specifically on short and branched chain acyl-CoA derivatives such as (S)-2-methylbutyryl-CoA as well as short straight chain acyl-CoAs such as butyryl-CoA (PubMed:7698750, PubMed:11013134, PubMed:21430231, PubMed:10832746). Plays an important role in the metabolism of L-isoleucine by catalyzing the dehydrogenation of 2-methylbutyryl-CoA, one of the steps of the L-isoleucine catabolic pathway (PubMed:11013134, PubMed:10832746). Can also act on valproyl-CoA, a metabolite of valproic acid, an antiepileptic drug (PubMed:8660691).<ref>PMID:10832746</ref> <ref>PMID:11013134</ref> <ref>PMID:21430231</ref> <ref>PMID:7698750</ref> <ref>PMID:8660691</ref>
+== 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/ji/2jif_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=2jif ConSurf].
+<div style="clear:both"></div>
+==See Also==
+*[[Acyl-CoA dehydrogenase 3D structures|Acyl-CoA dehydrogenase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Arrowsmith, C.H.]]
+[[Category: Arrowsmith CH]]
-[[Category: Delft, F.Von.]]
+[[Category: Edwards A]]
-[[Category: Edwards, A.]]
+[[Category: Hozjan V]]
-[[Category: Hozjan, V.]]
+[[Category: Kavanagh KL]]
-[[Category: Kavanagh, K.L.]]
+[[Category: Niesen FH]]
-[[Category: Niesen, F.H.]]
+[[Category: Oppermann U]]
-[[Category: Oppermann, U.]]
+[[Category: Pike ACW]]
-[[Category: Pike, A.C.W.]]
+[[Category: Smee C]]
-[[Category: Smee, C.]]
+[[Category: Sundstrom M]]
-[[Category: Sundstrom, M.]]
+[[Category: Turnbull AP]]
-[[Category: Turnbull, A.P.]]
+[[Category: Umeano C]]
-[[Category: Umeano, C.]]
+[[Category: Weigelt J]]
-[[Category: Weigelt, J.]]
+[[Category: Von Delft F]]
-[[Category: CL]]
-[[Category: COS]]
-[[Category: EDO]]
-[[Category: FAD]]
-[[Category: acetylation]]
-[[Category: disease mutation]]
-[[Category: fad]]
-[[Category: fatty acid metabolism]]
-[[Category: flavoprotein]]
-[[Category: lipid metabolism]]
-[[Category: mitochondrion]]
-[[Category: oxidoreductase]]
-[[Category: polymorphism]]
-[[Category: transit peptide]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Oct 30 17:35:05 2007''

2jif: Difference between revisions

Latest revision as of 14:50, 13 December 2023

Structure of human short-branched chain acyl-CoA dehydrogenase (ACADSB)

Structural highlights

Disease

Function

Evolutionary Conservation

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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