3dlx: Difference between revisions

Revision as of 14:11, 18 December 2014

Crystal structure of human 3-oxoacid CoA transferase 1

Structural highlights

3dlx 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.
Ligands:	GOL
Gene:	OXCT1, OXCT, SCOT (Homo sapiens)
Activity:	3-oxoacid CoA-transferase, with EC number 2.8.3.5
Resources:	FirstGlance, OCA, RCSB, PDBsum

Disease

[SCOT_HUMAN] Defects in OXCT1 are a cause of succinyl-CoA-3-ketoacid-CoA transferase deficiency (SCOTD) [MIM:245050]. A disorder of ketone body metabolism, characterized by episodic ketoacidosis. Patients are usually asymptomatic between episodes.^[1] ^[2] ^[3]

Function

[SCOT_HUMAN] Key enzyme for ketone body catabolism. Transfers the CoA moiety from succinate to acetoacetate. Formation of the enzyme-CoA intermediate proceeds via an unstable anhydride species formed between the carboxylate groups of the enzyme and substrate.

Evolutionary Conservation

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

References

↑ Fukao T, Mitchell GA, Song XQ, Nakamura H, Kassovska-Bratinova S, Orii KE, Wraith JE, Besley G, Wanders RJ, Niezen-Koning KE, Berry GT, Palmieri M, Kondo N. Succinyl-CoA:3-ketoacid CoA transferase (SCOT): cloning of the human SCOT gene, tertiary structural modeling of the human SCOT monomer, and characterization of three pathogenic mutations. Genomics. 2000 Sep 1;68(2):144-51. PMID:10964512 doi:10.1006/geno.2000.6282
↑ Song XQ, Fukao T, Watanabe H, Shintaku H, Hirayama K, Kassovska-Bratinova S, Kondo N, Mitchell GA. Succinyl-CoA:3-ketoacid CoA transferase (SCOT) deficiency: two pathogenic mutations, V133E and C456F, in Japanese siblings. Hum Mutat. 1998;12(2):83-8. PMID:9671268 doi:<83::AID-HUMU2>3.0.CO;2-P 10.1002/(SICI)1098-1004(1998)12:2<83::AID-HUMU2>3.0.CO;2-P
↑ Fukao T, Sass JO, Kursula P, Thimm E, Wendel U, Ficicioglu C, Monastiri K, Guffon N, Baric I, Zabot MT, Kondo N. Clinical and molecular characterization of five patients with succinyl-CoA:3-ketoacid CoA transferase (SCOT) deficiency. Biochim Biophys Acta. 2011 May;1812(5):619-24. doi: 10.1016/j.bbadis.2011.01.015., Epub 2011 Feb 2. PMID:21296660 doi:10.1016/j.bbadis.2011.01.015

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Fukao T, Mitchell GA, Song XQ, Nakamura H, Kassovska-Bratinova S, Orii KE, Wraith JE, Besley G, Wanders RJ, Niezen-Koning KE, Berry GT, Palmieri M, Kondo N. Succinyl-CoA:3-ketoacid CoA transferase (SCOT): cloning of the human SCOT gene, tertiary structural modeling of the human SCOT monomer, and characterization of three pathogenic mutations. Genomics. 2000 Sep 1;68(2):144-51. PMID:10964512 doi:10.1006/geno.2000.6282

[2] Song XQ, Fukao T, Watanabe H, Shintaku H, Hirayama K, Kassovska-Bratinova S, Kondo N, Mitchell GA. Succinyl-CoA:3-ketoacid CoA transferase (SCOT) deficiency: two pathogenic mutations, V133E and C456F, in Japanese siblings. Hum Mutat. 1998;12(2):83-8. PMID:9671268 doi:<83::AID-HUMU2>3.0.CO;2-P 10.1002/(SICI)1098-1004(1998)12:2<83::AID-HUMU2>3.0.CO;2-P

[3] Fukao T, Sass JO, Kursula P, Thimm E, Wendel U, Ficicioglu C, Monastiri K, Guffon N, Baric I, Zabot MT, Kondo N. Clinical and molecular characterization of five patients with succinyl-CoA:3-ketoacid CoA transferase (SCOT) deficiency. Biochim Biophys Acta. 2011 May;1812(5):619-24. doi: 10.1016/j.bbadis.2011.01.015., Epub 2011 Feb 2. PMID:21296660 doi:10.1016/j.bbadis.2011.01.015

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-{{STRUCTURE_3dlx|  PDB=3dlx  |  SCENE=  }}
+==Crystal structure of human 3-oxoacid CoA transferase 1==
-===Crystal structure of human 3-oxoacid CoA transferase 1===
+<StructureSection load='3dlx' size='340' side='right' caption='[[3dlx]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
-==Disease==
+<table><tr><td colspan='2'>[[3dlx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DLX FirstGlance]. <br>
-[[http://www.uniprot.org/uniprot/SCOT_HUMAN SCOT_HUMAN]] Defects in OXCT1 are a cause of succinyl-CoA-3-ketoacid-CoA transferase deficiency (SCOTD) [MIM:[http://omim.org/entry/245050 245050]]. A disorder of ketone body metabolism, characterized by episodic ketoacidosis. Patients are usually asymptomatic between episodes.<ref>PMID:10964512</ref><ref>PMID:9671268</ref><ref>PMID:21296660</ref>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">OXCT1, OXCT, SCOT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-==Function==
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-oxoacid_CoA-transferase 3-oxoacid CoA-transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.8.3.5 2.8.3.5] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3dlx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dlx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dlx RCSB], [http://www.ebi.ac.uk/pdbsum/3dlx PDBsum]</span></td></tr>
+</table>
+== Disease ==
+[[http://www.uniprot.org/uniprot/SCOT_HUMAN SCOT_HUMAN]] Defects in OXCT1 are a cause of succinyl-CoA-3-ketoacid-CoA transferase deficiency (SCOTD) [MIM:[http://omim.org/entry/245050 245050]]. A disorder of ketone body metabolism, characterized by episodic ketoacidosis. Patients are usually asymptomatic between episodes.<ref>PMID:10964512</ref> <ref>PMID:9671268</ref> <ref>PMID:21296660</ref>
+== Function ==
 [[http://www.uniprot.org/uniprot/SCOT_HUMAN SCOT_HUMAN]] Key enzyme for ketone body catabolism. Transfers the CoA moiety from succinate to acetoacetate. Formation of the enzyme-CoA intermediate proceeds via an unstable anhydride species formed between the carboxylate groups of the enzyme and substrate.
+== Evolutionary Conservation ==
-==About this Structure==
+[[Image:Consurf_key_small.gif|200px|right]]
-[[3dlx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLX OCA].
+Check<jmol>
+  <jmolCheckbox>
-==Reference==
+    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/3dlx_consurf.spt"</scriptWhenChecked>
-<references group="xtra"/><references/>
+    <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/chain_selection.php?pdb_ID=2ata ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: 3-oxoacid CoA-transferase]]
 [[Category: Homo sapiens]]
-[[Category: Arrowsmith, C H.]]
+[[Category: Arrowsmith, C H]]
-[[Category: Bountra, C.]]
+[[Category: Bountra, C]]
-[[Category: Delft, F von.]]
+[[Category: Delft, F von]]
-[[Category: Edwards, A M.]]
+[[Category: Edwards, A M]]
-[[Category: Kavanagh, K L.]]
+[[Category: Kavanagh, K L]]
-[[Category: Maclean, E M.]]
+[[Category: Maclean, E M]]
-[[Category: Murray, J W.]]
+[[Category: Murray, J W]]
-[[Category: Oppermann, U.]]
+[[Category: Oppermann, U]]
-[[Category: Picaud, S.]]
+[[Category: Picaud, S]]
-[[Category: Roos, A K.]]
+[[Category: Roos, A K]]
-[[Category: SGC, Structural Genomics Consortium.]]
+[[Category: Structural genomic]]
-[[Category: Shafqat, N.]]
+[[Category: Shafqat, N]]
-[[Category: Wikstrom, M.]]
+[[Category: Wikstrom, M]]
-[[Category: Yue, W W.]]
+[[Category: Yue, W W]]
 [[Category: Disease mutation]]
 [[Category: Mitochondrion]]
@@ Line 34: / Line 47: @@
 [[Category: Scot]]
 [[Category: Sgc]]
-[[Category: Structural genomic]]
-[[Category: Structural genomics consortium]]
 [[Category: Succinyl-coa:3-ketoacid-coenzyme a transferase 1]]
 [[Category: Transferase]]
 [[Category: Transit peptide]]

3dlx: Difference between revisions

Revision as of 14:11, 18 December 2014

Crystal structure of human 3-oxoacid CoA transferase 1

Structural highlights

Disease

Function

Evolutionary Conservation

References

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