3ms5: Difference between revisions

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<StructureSection load='3ms5' size='340' side='right'caption='[[3ms5]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
<StructureSection load='3ms5' size='340' side='right'caption='[[3ms5]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ms5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MS5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MS5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ms5]] is a 1 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=3MS5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MS5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=REE:2-(2-CARBOXYETHYL)-1,1,1-TRIMETHYLDIAZANIUM'>REE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.82&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BBH, BBOX, BBOX1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=REE:2-(2-CARBOXYETHYL)-1,1,1-TRIMETHYLDIAZANIUM'>REE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Gamma-butyrobetaine_dioxygenase Gamma-butyrobetaine dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.1 1.14.11.1] </span></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=3ms5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ms5 OCA], [https://pdbe.org/3ms5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ms5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ms5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ms5 ProSAT]</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=3ms5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ms5 OCA], [http://pdbe.org/3ms5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ms5 RCSB], [http://www.ebi.ac.uk/pdbsum/3ms5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ms5 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/BODG_HUMAN BODG_HUMAN]] Catalyzes the formation of L-carnitine from gamma-butyrobetaine.  
[https://www.uniprot.org/uniprot/BODG_HUMAN BODG_HUMAN] Catalyzes the formation of L-carnitine from gamma-butyrobetaine.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=3ms5 ConSurf].
</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=3ms5 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The final step in carnitine biosynthesis is catalyzed by gamma-butyrobetaine (gammaBB) hydroxylase (BBOX), an iron/2-oxoglutarate (2OG) dependent oxygenase. BBOX is inhibited by trimethylhydrazine-propionate (THP), a clinically used compound. We report structural and mechanistic studies on BBOX and its reaction with THP. Crystallographic and sequence analyses reveal that BBOX and trimethyllysine hydroxylase form a subfamily of 2OG oxygenases that dimerize using an N-terminal domain. The crystal structure reveals the active site is enclosed and how THP competes with gammaBB. THP is a substrate giving formaldehyde (supporting structural links with histone demethylases), dimethylamine, malonic acid semi-aldehyde, and an unexpected product with an additional carbon-carbon bond resulting from N-demethylation coupled to oxidative rearrangement, likely via an unusual radical mechanism. The results provide a basis for development of improved BBOX inhibitors and may inspire the discovery of additional rearrangement reactions.


Structural and mechanistic studies on gamma-butyrobetaine hydroxylase.,Leung IK, Krojer TJ, Kochan GT, Henry L, von Delft F, Claridge TD, Oppermann U, McDonough MA, Schofield CJ Chem Biol. 2010 Dec 22;17(12):1316-24. PMID:21168767<ref>PMID:21168767</ref>
==See Also==
 
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ms5" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Gamma-butyrobetaine dioxygenase]]
[[Category: Homo sapiens]]
[[Category: Human]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Arrowsmith, C H]]
[[Category: Arrowsmith CH]]
[[Category: Bountra, C]]
[[Category: Bountra C]]
[[Category: Claridge, T D.W]]
[[Category: Claridge TDW]]
[[Category: Delft, F von]]
[[Category: Edwards A]]
[[Category: Edwards, A]]
[[Category: Filippakopoulos P]]
[[Category: Filippakopoulos, P]]
[[Category: Henry L]]
[[Category: Henry, L]]
[[Category: Kavanagh KL]]
[[Category: Kavanagh, K L]]
[[Category: Kochan G]]
[[Category: Kochan, G]]
[[Category: Krojer T]]
[[Category: Krojer, T]]
[[Category: Leung IKH]]
[[Category: Leung, I K.H]]
[[Category: McDonough MA]]
[[Category: McDonough, M A]]
[[Category: Muniz J]]
[[Category: Muniz, J]]
[[Category: Oppermann U]]
[[Category: Oppermann, U]]
[[Category: Pilka E]]
[[Category: Pilka, E]]
[[Category: Schofield CJ]]
[[Category: Structural genomic]]
[[Category: Ugochukwu E]]
[[Category: Schofield, C J]]
[[Category: Weigelt J]]
[[Category: Ugochukwu, E]]
[[Category: Von Delft F]]
[[Category: Weigelt, J]]
[[Category: 2-oxoglutarate dioxygenase 1]]
[[Category: Gamma-butyrobetaine]]
[[Category: Gamma-butyrobetaine hydroxylase]]
[[Category: Oxidoreductase]]
[[Category: Sgc]]
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