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6i4t

From Proteopedia

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Current revision

Crystal structure of the disease-causing I445M mutant of the human dihydrolipoamide dehydrogenase

Structural highlights

6i4t is a 2 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 1.823Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

DLDH_HUMAN Note=Defects in DLD are involved in the development of congenital infantile lactic acidosis. Defects in DLD are a cause of maple syrup urine disease (MSUD) [MIM:248600. MSUD is characterized by mental and physical retardation, feeding problems and a maple syrup odor to the urine. The keto acids of the branched-chain amino acids are present in the urine, resulting from a block in oxidative decarboxylation.

Function

DLDH_HUMAN Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes. Involved in the hyperactivation of spermatazoa during capacitation and in the spermatazoal acrosome reaction.

Publication Abstract from PubMed

Human dihydrolipoamide dehydrogenase (hLADH, hE3) deficiency (OMIM# 246900) is an often prematurely lethal genetic disease usually caused by inactive or partially inactive hE3 variants. Here we report the crystal structure of wild-type hE3 at an unprecedented high resolution of 1.75 A and the structures of six disease-causing hE3 variants at resolutions ranging from 1.44 to 2.34 A. P453L proved to be the most deleterious substitution in structure as aberrations extensively compromised the active site. The most prevalent G194C-hE3 variant primarily exhibited structural alterations close to the substitution site, whereas the nearby cofactor-binding residues were left unperturbed. The G426E substitution mainly interfered with the local charge distribution introducing dynamics to the substitution site in the dimer interface; G194C and G426E both led to minor structural changes. The R460G, R447G, and I445M substitutions all perturbed a solvent accessible channel, the so-called H+/H2O channel, leading to the active site. Molecular pathomechanisms of enhanced reactive oxygen species (ROS) generation and impaired binding to multienzyme complexes were also addressed according to the structural data for the relevant mutations. In summary, we present here for the first time a comprehensive study that links three-dimensional structures of disease-causing hE3 variants to residual hLADH activities, altered capacities for ROS generation, compromised affinities for multienzyme complexes, and eventually clinical symptoms. Our results may serve as useful starting points for future therapeutic intervention approaches.

Underlying molecular alterations in human dihydrolipoamide dehydrogenase deficiency revealed by structural analyses of disease-causing enzyme variants.,Szabo E, Wilk P, Nagy B, Zambo Z, Bui D, Weichsel A, Arjunan P, Torocsik B, Hubert A, Furey W, Montfort WR, Jordan F, Weiss MS, Adam-Vizi V, Ambrus A Hum Mol Genet. 2019 Jul 23. pii: 5537123. doi: 10.1093/hmg/ddz177. PMID:31334547^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Szabo E, Wilk P, Nagy B, Zambo Z, Bui D, Weichsel A, Arjunan P, Torocsik B, Hubert A, Furey W, Montfort WR, Jordan F, Weiss MS, Adam-Vizi V, Ambrus A. Underlying molecular alterations in human dihydrolipoamide dehydrogenase deficiency revealed by structural analyses of disease-causing enzyme variants. Hum Mol Genet. 2019 Jul 23. pii: 5537123. doi: 10.1093/hmg/ddz177. PMID:31334547 doi:http://dx.doi.org/10.1093/hmg/ddz177

1 Structural highlights
2 Disease
3 Function
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6i4t"

@@ Line 3: / Line 3: @@
 <StructureSection load='6i4t' size='340' side='right'caption='[[6i4t]], [[Resolution|resolution]] 1.82&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6i4t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I4T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6i4t]] is a 2 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=6I4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I4T FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.823&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrolipoyl_dehydrogenase Dihydrolipoyl dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.4 1.8.1.4] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6i4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i4t OCA], [http://pdbe.org/6i4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i4t RCSB], [http://www.ebi.ac.uk/pdbsum/6i4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i4t ProSAT]</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=6i4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i4t OCA], [https://pdbe.org/6i4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i4t RCSB], [https://www.ebi.ac.uk/pdbsum/6i4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i4t ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/DLDH_HUMAN DLDH_HUMAN]] Note=Defects in DLD are involved in the development of congenital infantile lactic acidosis.  Defects in DLD are a cause of maple syrup urine disease (MSUD) [MIM:[http://omim.org/entry/248600 248600]]. MSUD is characterized by mental and physical retardation, feeding problems and a maple syrup odor to the urine. The keto acids of the branched-chain amino acids are present in the urine, resulting from a block in oxidative decarboxylation.
+[https://www.uniprot.org/uniprot/DLDH_HUMAN DLDH_HUMAN] Note=Defects in DLD are involved in the development of congenital infantile lactic acidosis.  Defects in DLD are a cause of maple syrup urine disease (MSUD) [MIM:[https://omim.org/entry/248600 248600]. MSUD is characterized by mental and physical retardation, feeding problems and a maple syrup odor to the urine. The keto acids of the branched-chain amino acids are present in the urine, resulting from a block in oxidative decarboxylation.
 == Function ==
-[[http://www.uniprot.org/uniprot/DLDH_HUMAN DLDH_HUMAN]] Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes. Involved in the hyperactivation of spermatazoa during capacitation and in the spermatazoal acrosome reaction.
+[https://www.uniprot.org/uniprot/DLDH_HUMAN DLDH_HUMAN] Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes. Involved in the hyperactivation of spermatazoa during capacitation and in the spermatazoal acrosome reaction.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 21: @@
 </div>
 <div class="pdbe-citations 6i4t" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Dihydrolipoamide dehydrogenase|Dihydrolipoamide dehydrogenase]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Dihydrolipoyl dehydrogenase]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Adam-Vizi, V]]
+[[Category: Adam-Vizi V]]
-[[Category: Ambrus, A]]
+[[Category: Ambrus A]]
-[[Category: Szabo, E]]
+[[Category: Szabo E]]
-[[Category: Torocsik, B]]
+[[Category: Torocsik B]]
-[[Category: Weiss, M S]]
+[[Category: Weiss MS]]
-[[Category: Wilk, P]]
+[[Category: Wilk P]]
-[[Category: Zambo, Z]]
+[[Category: Zambo Z]]
-[[Category: 2-oxoglutarate dehydrogenase complex]]
-[[Category: Alpha-ketoglutarate dehydrogenase complex]]
-[[Category: E3 deficiency]]
-[[Category: Lipoamide dehydrogenase]]
-[[Category: Oxidoreductase]]
-[[Category: Pathogenic mutation]]
-[[Category: Pyruvate dehydrogenase complex]]

6i4t

From Proteopedia

Current revision

Crystal structure of the disease-causing I445M mutant of the human dihydrolipoamide dehydrogenase

Structural highlights

Disease

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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