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3mp5

From Proteopedia

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Crystal Structure of Human Lyase R41M in complex with HMG-CoA

Structural highlights

3mp5 is a 6 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 2.25Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

HMGCL_HUMAN Defects in HMGCL are the cause of 3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD) [MIM:246450; also known as hydroxymethylglutaricaciduria or HL deficiency. An autosomal recessive disease affecting ketogenesis and L-leucine catabolism. The disease usually appears in the first year of life after a fasting period and its clinical acute symptoms include vomiting, seizures, metabolic acidosis, hypoketotic hypoglycemia and lethargy. These symptoms sometimes progress to coma, with fatal outcome in some cases.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10]

Function

HMGCL_HUMAN Key enzyme in ketogenesis (ketone body formation). Terminal step in leucine catabolism.^[11] ^[12] ^[13]

Evolutionary Conservation

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

Publication Abstract from PubMed

HMG-CoA lyase (HMGCL) is crucial to ketogenesis, and inherited human mutations are potentially lethal. Detailed understanding of the HMGCL reaction mechanism and the molecular basis for correlating human mutations with enzyme deficiency have been limited by the lack of structural information for enzyme liganded to an acyl-CoA substrate or inhibitor. Crystal structures of ternary complexes of WT HMGCL with the competitive inhibitor 3-hydroxyglutaryl-CoA and of the catalytically deficient HMGCL R41M mutant with substrate HMG-CoA have been determined to 2.4 and 2.2 A, respectively. Comparison of these beta/alpha-barrel structures with those of unliganded HMGCL and R41M reveals substantial differences for Mg(2+) coordination and positioning of the flexible loop containing the conserved HMGCL "signature" sequence. In the R41M-Mg(2+)-substrate ternary complex, loop residue Cys(266) (implicated in active-site function by mechanistic and mutagenesis observations) is more closely juxtaposed to the catalytic site than in the case of unliganded enzyme or the WT enzyme-Mg(2+)-3-hydroxyglutaryl-CoA inhibitor complex. In both ternary complexes, the S-stereoisomer of substrate or inhibitor is specifically bound, in accord with the observed Mg(2+) liganding of both C3 hydroxyl and C5 carboxyl oxygens. In addition to His(233) and His(235) imidazoles, other Mg(2+) ligands are the Asp(42) carboxyl oxygen and an ordered water molecule. This water, positioned between Asp(42) and the C3 hydroxyl of bound substrate/inhibitor, may function as a proton shuttle. The observed interaction of Arg(41) with the acyl-CoA C1 carbonyl oxygen explains the effects of Arg(41) mutation on reaction product enolization and explains why human Arg(41) mutations cause drastic enzyme deficiency.

Functional insights into human HMG-CoA lyase from structures of Acyl-CoA-containing ternary complexes.,Fu Z, Runquist JA, Montgomery C, Miziorko HM, Kim JJ J Biol Chem. 2010 Aug 20;285(34):26341-9. Epub 2010 Jun 17. PMID:20558737^[14]

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

References

↑ Roberts JR, Mitchell GA, Miziorko HM. Modeling of a mutation responsible for human 3-hydroxy-3-methylglutaryl-CoA lyase deficiency implicates histidine 233 as an active site residue. J Biol Chem. 1996 Oct 4;271(40):24604-9. PMID:8798725
↑ Mitchell GA, Ozand PT, Robert MF, Ashmarina L, Roberts J, Gibson KM, Wanders RJ, Wang S, Chevalier I, Plochl E, Miziorko H. HMG CoA lyase deficiency: identification of five causal point mutations in codons 41 and 42, including a frequent Saudi Arabian mutation, R41Q. Am J Hum Genet. 1998 Feb;62(2):295-300. PMID:9463337 doi:10.1086/301730
↑ Zapater N, Pie J, Lloberas J, Rolland MO, Leroux B, Vidailhet M, Divry P, Hegardt FG, Casals N. Two missense point mutations in different alleles in the 3-hydroxy-3-methylglutaryl coenzyme A lyase gene produce 3-hydroxy-3-methylglutaric aciduria in a French patient. Arch Biochem Biophys. 1998 Oct 15;358(2):197-203. PMID:9784232 doi:S0003-9861(98)90788-3
↑ Muroi J, Yorifuji T, Uematsu A, Shigematsu Y, Onigata K, Maruyama H, Nobutoki T, Kitamura A, Nakahata T. Molecular and clinical analysis of Japanese patients with 3-hydroxy-3-methylglutaryl CoA lyase (HL) deficiency. Hum Genet. 2000 Oct;107(4):320-6. PMID:11129331
↑ Casals N, Gomez-Puertas P, Pie J, Mir C, Roca R, Puisac B, Aledo R, Clotet J, Menao S, Serra D, Asins G, Till J, Elias-Jones AC, Cresto JC, Chamoles NA, Abdenur JE, Mayatepek E, Besley G, Valencia A, Hegardt FG. Structural (betaalpha)8 TIM barrel model of 3-hydroxy-3-methylglutaryl-coenzyme A lyase. J Biol Chem. 2003 Aug 1;278(31):29016-23. Epub 2003 May 13. PMID:12746442 doi:10.1074/jbc.M304276200
↑ Al-Sayed M, Imtiaz F, Alsmadi OA, Rashed MS, Meyer BF. Mutations underlying 3-hydroxy-3-methylglutaryl CoA lyase deficiency in the Saudi population. BMC Med Genet. 2006 Dec 16;7:86. PMID:17173698 doi:10.1186/1471-2350-7-86
↑ Mir C, Lopez-Vinas E, Aledo R, Puisac B, Rizzo C, Dionisi-Vici C, Deodato F, Pie J, Gomez-Puertas P, Hegardt FG, Casals N. A single-residue mutation, G203E, causes 3-hydroxy-3-methylglutaric aciduria by occluding the substrate channel in the 3D structural model of HMG-CoA lyase. J Inherit Metab Dis. 2006 Feb;29(1):64-70. PMID:16601870 doi:10.1007/s10545-006-0138-x
↑ Carrasco P, Menao S, Lopez-Vinas E, Santpere G, Clotet J, Sierra AY, Gratacos E, Puisac B, Gomez-Puertas P, Hegardt FG, Pie J, Casals N. C-terminal end and aminoacid Lys48 in HMG-CoA lyase are involved in substrate binding and enzyme activity. Mol Genet Metab. 2007 Jun;91(2):120-7. Epub 2007 Apr 24. PMID:17459752 doi:10.1016/j.ymgme.2007.03.007
↑ Lin WD, Wang CH, Lai CC, Tsai Y, Wu JY, Chen CP, Tsai FJ. Molecular analysis of Taiwanese patients with 3-hydroxy-3-methylglutaryl CoA lyase deficiency. Clin Chim Acta. 2009 Mar;401(1-2):33-6. doi: 10.1016/j.cca.2008.11.004. Epub 2008, Nov 12. PMID:19036343 doi:10.1016/j.cca.2008.11.004
↑ Menao S, Lopez-Vinas E, Mir C, Puisac B, Gratacos E, Arnedo M, Carrasco P, Moreno S, Ramos M, Gil MC, Pie A, Ribes A, Perez-Cerda C, Ugarte M, Clayton PT, Korman SH, Serra D, Asins G, Ramos FJ, Gomez-Puertas P, Hegardt FG, Casals N, Pie J. Ten novel HMGCL mutations in 24 patients of different origin with 3-hydroxy-3-methyl-glutaric aciduria. Hum Mutat. 2009 Mar;30(3):E520-9. doi: 10.1002/humu.20966. PMID:19177531 doi:10.1002/humu.20966
↑ Holmes HC, Burns SP, Chalmers RA, Bain MS, Iles RA. Ketogenic flux from lipids and leucine, assessment in 3-hydroxy-3-methylglutaryl CoA lyase deficiency. Biochem Soc Trans. 1995 Aug;23(3):489S. PMID:8566388
↑ Montgomery C, Pei Z, Watkins PA, Miziorko HM. Identification and characterization of an extramitochondrial human 3-hydroxy-3-methylglutaryl-CoA lyase. J Biol Chem. 2012 Sep 28;287(40):33227-36. Epub 2012 Aug 3. PMID:22865860 doi:10.1074/jbc.M112.393231
↑ Arnedo M, Menao S, Puisac B, Teresa-Rodrigo ME, Gil-Rodriguez MC, Lopez-Vinas E, Gomez-Puertas P, Casals N, Casale CH, Hegardt FG, Pie J. Characterization of a novel HMG-CoA lyase enzyme with a dual location in endoplasmic reticulum and cytosol. J Lipid Res. 2012 Oct;53(10):2046-56. doi: 10.1194/jlr.M025700. Epub 2012 Jul 30. PMID:22847177 doi:10.1194/jlr.M025700
↑ Fu Z, Runquist JA, Montgomery C, Miziorko HM, Kim JJ. Functional insights into human HMG-CoA lyase from structures of Acyl-CoA-containing ternary complexes. J Biol Chem. 2010 Aug 20;285(34):26341-9. Epub 2010 Jun 17. PMID:20558737 doi:10.1074/jbc.M110.139931

1 Structural highlights
2 Disease
3 Function
4 Evolutionary Conservation
5 Publication Abstract from PubMed
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3mp5"

@@ Line 3: / Line 3: @@
 <StructureSection load='3mp5' size='340' side='right'caption='[[3mp5]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3mp5]] is a 6 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=3MP5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MP5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3mp5]] is a 6 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=3MP5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MP5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HMG:3-HYDROXY-3-METHYLGLUTARYL-COENZYME+A'>HMG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.25&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3mp3|3mp3]], [[3mp4|3mp4]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HMG:3-HYDROXY-3-METHYLGLUTARYL-COENZYME+A'>HMG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HMGCL ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Hydroxymethylglutaryl-CoA_lyase Hydroxymethylglutaryl-CoA lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.4 4.1.3.4] </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=3mp5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mp5 OCA], [https://pdbe.org/3mp5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mp5 RCSB], [https://www.ebi.ac.uk/pdbsum/3mp5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mp5 ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[https://www.uniprot.org/uniprot/HMGCL_HUMAN HMGCL_HUMAN]] Defects in HMGCL are the cause of 3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD) [MIM:[https://omim.org/entry/246450 246450]]; also known as hydroxymethylglutaricaciduria or HL deficiency. An autosomal recessive disease affecting ketogenesis and L-leucine catabolism. The disease usually appears in the first year of life after a fasting period and its clinical acute symptoms include vomiting, seizures, metabolic acidosis, hypoketotic hypoglycemia and lethargy. These symptoms sometimes progress to coma, with fatal outcome in some cases.<ref>PMID:8798725</ref> <ref>PMID:9463337</ref> <ref>PMID:9784232</ref> <ref>PMID:11129331</ref> <ref>PMID:12746442</ref> <ref>PMID:17173698</ref> <ref>PMID:16601870</ref> <ref>PMID:17459752</ref> <ref>PMID:19036343</ref> <ref>PMID:19177531</ref>
+[https://www.uniprot.org/uniprot/HMGCL_HUMAN HMGCL_HUMAN] Defects in HMGCL are the cause of 3-hydroxy-3-methylglutaryl-CoA lyase deficiency (HMGCLD) [MIM:[https://omim.org/entry/246450 246450]; also known as hydroxymethylglutaricaciduria or HL deficiency. An autosomal recessive disease affecting ketogenesis and L-leucine catabolism. The disease usually appears in the first year of life after a fasting period and its clinical acute symptoms include vomiting, seizures, metabolic acidosis, hypoketotic hypoglycemia and lethargy. These symptoms sometimes progress to coma, with fatal outcome in some cases.<ref>PMID:8798725</ref> <ref>PMID:9463337</ref> <ref>PMID:9784232</ref> <ref>PMID:11129331</ref> <ref>PMID:12746442</ref> <ref>PMID:17173698</ref> <ref>PMID:16601870</ref> <ref>PMID:17459752</ref> <ref>PMID:19036343</ref> <ref>PMID:19177531</ref>
 == Function ==
-[[https://www.uniprot.org/uniprot/HMGCL_HUMAN HMGCL_HUMAN]] Key enzyme in ketogenesis (ketone body formation). Terminal step in leucine catabolism.<ref>PMID:8566388</ref> <ref>PMID:22865860</ref> <ref>PMID:22847177</ref>
+[https://www.uniprot.org/uniprot/HMGCL_HUMAN HMGCL_HUMAN] Key enzyme in ketogenesis (ketone body formation). Terminal step in leucine catabolism.<ref>PMID:8566388</ref> <ref>PMID:22865860</ref> <ref>PMID:22847177</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Hydroxymethylglutaryl-CoA lyase]]
 [[Category: Large Structures]]
-[[Category: Fu, Z]]
+[[Category: Fu Z]]
-[[Category: Kim, J J.P]]
+[[Category: Kim J-JP]]
-[[Category: Miziorko, H M]]
+[[Category: Miziorko HM]]
-[[Category: Montgomery, C]]
+[[Category: Montgomery C]]
-[[Category: Runquist, J A]]
+[[Category: Runquist JA]]
-[[Category: 3-hydroxyl-3-methylglutaryl-coa]]
-[[Category: Human hmg-coa lyase]]
-[[Category: Ketogenic enzyme]]
-[[Category: Lyase]]

3mp5

From Proteopedia

Current revision

Crystal Structure of Human Lyase R41M in complex with HMG-CoA

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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