6lpp: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older editNewer edit →
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
Line 1: Line 1:


==Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-2-hydroxyglutarate (D-2-HG)==
==Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-2-hydroxyglutarate (D-2-HG)==
<StructureSection load='6lpp' size='340' side='right'caption='[[6lpp]]' scene=''>
<StructureSection load='6lpp' size='340' side='right'caption='[[6lpp]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LPP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LPP FirstGlance]. <br>
<table><tr><td colspan='2'>[[6lpp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LPP FirstGlance]. <br>
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6lpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lpp OCA], [http://pdbe.org/6lpp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lpp RCSB], [http://www.ebi.ac.uk/pdbsum/6lpp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lpp ProSAT]</span></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2HG:(2R)-2-HYDROXYPENTANEDIOIC+ACID'>2HG</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">D2HGDH, D2HGD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6lpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lpp OCA], [https://pdbe.org/6lpp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lpp RCSB], [https://www.ebi.ac.uk/pdbsum/6lpp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lpp ProSAT]</span></td></tr>
</table>
</table>
== Disease ==
[[https://www.uniprot.org/uniprot/D2HDH_HUMAN D2HDH_HUMAN]] D-2-hydroxyglutaric aciduria. The disease is caused by variants affecting the gene represented in this entry.
== Function ==
[[https://www.uniprot.org/uniprot/D2HDH_HUMAN D2HDH_HUMAN]] Catalyzes the oxidation of D-2-hydroxyglutarate to alpha-ketoglutarate.<ref>PMID:15070399</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
D-2-hydroxyglutarate dehydrogenase (D-2-HGDH) catalyzes the oxidation of D-2-hydroxyglutarate (D-2-HG) into 2-oxoglutarate, and genetic D-2-HGDH deficiency leads to abnormal accumulation of D-2-HG which causes type I D-2-hydroxyglutaric aciduria and is associated with diffuse large B-cell lymphoma. This work reports the crystal structures of human D-2-HGDH in apo form and in complexes with D-2-HG, D-malate, D-lactate, L-2-HG, and 2-oxoglutarate, respectively. D-2-HGDH comprises a FAD-binding domain, a substrate-binding domain, and a small C-terminal domain. The active site is located at the interface of the FAD-binding domain and the substrate-binding domain. The functional roles of the key residues involved in the substrate binding and catalytic reaction and the mutations identified in D-2-HGDH-deficient diseases are analyzed by biochemical studies. The structural and biochemical data together reveal the molecular mechanism of the substrate specificity and catalytic reaction of D-2-HGDH and provide insights into the pathogenicity of the disease-associated mutations.
Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations.,Yang J, Zhu H, Zhang T, Ding J Cell Discov. 2021 Jan 12;7(1):3. doi: 10.1038/s41421-020-00227-0. PMID:33431826<ref>PMID:33431826</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6lpp" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ding J]]
[[Category: Ding, J]]
[[Category: Yang J]]
[[Category: Yang, J]]
[[Category: Zhu H]]
[[Category: Zhu, H]]
[[Category: Dehydrogenase]]
[[Category: Flavoprotein]]
[[Category: Oxidoreductase]]
Retrieved from "https://proteopedia.org/6lpp"