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Oxidoreductase PDB id
1dtw
Jmol
Contents
Protein chains
382 a.a. *
326 a.a. *
Ligands
TDP
Metals
__K ×2
_MG
Waters ×48
* Residue conservation analysis
PDB id:
1dtw
Name: Oxidoreductase
Title: Human branched-chain alpha-keto acid dehydrogenase
Structure: Branched-chain alpha-keto acid dehydrogenase alph chain: a. Engineered: yes. Branched-chain alpha-keto acid dehydrogenase beta chain: b. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.70Å     R-factor:   0.224     R-free:   0.279
Authors: A.Aevarsson,J.L.Chuang,R.M.Wynn,S.Turley,D.T.Chuang,W.G.J.Ho
Key ref:
A.AEvarsson et al. (2000). Crystal structure of human branched-chain alpha-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease. Structure, 8, 277-291. PubMed id: 10745006 DOI: 10.1016/S0969-2126(00)00105-2
Date:
13-Jan-00     Release date:   27-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P12694  (ODBA_HUMAN) -  2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial
Seq:
Struc: 		445 a.a.
382 a.a.
Protein chain
Pfam   ArchSchema ?
P21953  (ODBB_HUMAN) -  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial
Seq:
Struc: 		392 a.a.
326 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.1.2.4.4  - 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Oxo-acid dehydrogenase complexes
      Reaction: 3-methyl-2-oxobutanoate + [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine = [dihydrolipoyllysine- residue (2-methylpropanoyl)transferase] S-(2-methylpropanoyl)dihydrolipoyllysine + CO2
3-methyl-2-oxobutanoate
 + [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine
 = [dihydrolipoyllysine- residue (2-methylpropanoyl)transferase] S-(2-methylpropanoyl)dihydrolipoyllysine
 + CO(2)
      Cofactor: Thiamine diphosphate
Thiamine diphosphate
Bound ligand (Het Group name = TDP) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrion   3 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(00)00105-2 Structure 8:277-291 (2000)
PubMed id: 10745006  
 
 
Crystal structure of human branched-chain alpha-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease.
A.AEvarsson, J.L.Chuang, R.M.Wynn, S.Turley, D.T.Chuang, W.G.Hol.
 
  ABSTRACT  
 
BACKGROUND: Mutations in components of the extraordinarily large alpha-ketoacid dehydrogenase multienzyme complexes can lead to serious and often fatal disorders in humans, including maple syrup urine disease (MSUD). In order to obtain insight into the effect of mutations observed in MSUD patients, we determined the crystal structure of branched-chain alpha-ketoacid dehydrogenase (E1), the 170 kDa alpha(2)beta(2) heterotetrameric E1b component of the branched-chain alpha-ketoacid dehydrogenase multienzyme complex. RESULTS: The 2.7 A resolution crystal structure of human E1b revealed essentially the full alpha and beta polypeptide chains of the tightly packed heterotetramer. The position of two important potassium (K(+)) ions was determined. One of these ions assists a loop that is close to the cofactor to adopt the proper conformation. The second is located in the beta subunit near the interface with the small C-terminal domain of the alpha subunit. The known MSUD mutations affect the functioning of E1b by interfering with the cofactor and K(+) sites, the packing of hydrophobic cores, and the precise arrangement of residues at or near several subunit interfaces. The Tyr-->Asn mutation at position 393-alpha occurs very frequently in the US population of Mennonites and is located in a unique extension of the human E1b alpha subunit, contacting the beta' subunit. CONCLUSIONS: Essentially all MSUD mutations in human E1b can be explained on the basis of the structure, with the severity of the mutations for the stability and function of the protein correlating well with the severity of the disease for the patients. The suggestion is made that small molecules with high affinity for human E1b might alleviate effects of some of the milder forms of MSUD.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Cofactor and K+-binding sites in human E1b. (a) Schematic representation of the cofactor-binding site. Gln112-a and protein ligands of the magnesium ion have been omitted for clarity. (b) Potassium site 1 (a subunit). The metal stabilizes a loop involved in cofactor binding. The metal ion is bound by two mainchain carbonyl groups and by the sidechains of Ser161-a, Thr166-a and Gln167-a. The sidechain of Leu164-a and the mainchain carbonyl group of Ser162-a make direct contact with the ThDP cofactor. (c) Potassium site 2 (b subunit). The metal binding at this site stabilizes regions in the b subunit at the interface with the small C-terminal domain in the a subunit. The metal is octahedrally coordinated mainly by mainchain carbonyl groups and interacts favorably with the C-terminal end of a helix dipole as indicated. Several sidechains indicated by an asterisk have been omitted for clarity. This figure was made with LIGPLOT [50], MOLSCRIPT [48] and the Raster3D suite [49].
 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 277-291) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19715473 T.Georgiou, J.L.Chuang, R.M.Wynn, G.Stylianidou, M.Korson, D.T.Chuang, and A.Drousiotou (2009).
Maple syrup urine disease in Cypriot families: identification of three novel mutations and biochemical characterization of the p.Thr211Met mutation in the E1alpha subunit.
  Genet Test Mol Biomarkers, 13, 657-664.  
18206651 L.G.Korotchkina, and M.S.Patel (2008).
Binding of pyruvate dehydrogenase to the core of the human pyruvate dehydrogenase complex.
  FEBS Lett, 582, 468-472.  
18316329 T.Nakai, S.Kuramitsu, and N.Kamiya (2008).
Structural bases for the specific interactions between the E2 and E3 components of the Thermus thermophilus 2-oxo acid dehydrogenase complexes.
  J Biochem, 143, 747-758.  
18783430 V.Bunik, T.Kaehne, D.Degtyarev, T.Shcherbakova, and G.Reiser (2008).
Novel isoenzyme of 2-oxoglutarate dehydrogenase is identified in brain, but not in heart.
  FEBS J, 275, 4990-5006.  
18004749 V.I.Bunik, and D.Degtyarev (2008).
Structure-function relationships in the 2-oxo acid dehydrogenase family: substrate-specific signatures and functional predictions for the 2-oxoglutarate dehydrogenase-like proteins.
  Proteins, 71, 874-890.  
18184588 X.Yu, Y.Hiromasa, H.Tsen, J.K.Stoops, T.E.Roche, and Z.H.Zhou (2008).
Structures of the human pyruvate dehydrogenase complex cores: a highly conserved catalytic center with flexible N-terminal domains.
  Structure, 16, 104-114.
PDB code: 3b8k
17391016 H.Xie, S.Vucetic, L.M.Iakoucheva, C.J.Oldfield, A.K.Dunker, Z.Obradovic, and V.N.Uversky (2007).
Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins.
  J Proteome Res, 6, 1917-1932.  
17329260 J.Li, M.Machius, J.L.Chuang, R.M.Wynn, and D.T.Chuang (2007).
The two active sites in human branched-chain alpha-keto acid dehydrogenase operate independently without an obligatory alternating-site mechanism.
  J Biol Chem, 282, 11904-11913.
PDB code: 2j9f
17314104 M.M.Islam, R.Wallin, R.M.Wynn, M.Conway, H.Fujii, J.A.Mobley, D.T.Chuang, and S.M.Hutson (2007).
A novel branched-chain amino acid metabolon. Protein-protein interactions in a supramolecular complex.
  J Biol Chem, 282, 11893-11903.  
17922217 N.Flaschker, O.Feyen, S.Fend, E.Simon, P.Schadewaldt, and U.Wendel (2007).
Description of the mutations in 15 subjects with variant forms of maple syrup urine disease.
  J Inherit Metab Dis, 30, 903-909.  
16267046 E.Di Cera (2006).
A structural perspective on enzymes activated by monovalent cations.
  J Biol Chem, 281, 1305-1308.  
17063375 E.Simon, N.Flaschker, P.Schadewaldt, U.Langenbeck, and U.Wendel (2006).
Variant maple syrup urine disease (MSUD)--the entire spectrum.
  J Inherit Metab Dis, 29, 716-724.  
15612915 B.J.Foth, L.M.Stimmler, E.Handman, B.S.Crabb, A.N.Hodder, and G.I.McFadden (2005).
The malaria parasite Plasmodium falciparum has only one pyruvate dehydrogenase complex, which is located in the apicoplast.
  Mol Microbiol, 55, 39-53.  
16216870 C.L.Berthold, P.Moussatche, N.G.Richards, and Y.Lindqvist (2005).
Structural basis for activation of the thiamin diphosphate-dependent enzyme oxalyl-CoA decarboxylase by adenosine diphosphate.
  J Biol Chem, 280, 41645-41654.
PDB code: 2c31
15634348 M.D.Allen, R.W.Broadhurst, R.G.Solomon, and R.N.Perham (2005).
Interaction of the E2 and E3 components of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus. Use of a truncated protein domain in NMR spectroscopy.
  FEBS J, 272, 259-268.
PDB code: 1w3d
16084384 R.A.Frank, J.V.Pratap, X.Y.Pei, R.N.Perham, and B.F.Luisi (2005).
The molecular origins of specificity in the assembly of a multienzyme complex.
  Structure, 13, 1119-1130.
PDB code: 2bp7
15752351 R.Golbik, L.E.Meshalkina, T.Sandalova, K.Tittmann, E.Fiedler, H.Neef, S.König, R.Kluger, G.A.Kochetov, G.Schneider, and G.Hübner (2005).
Effect of coenzyme modification on the structural and catalytic properties of wild-type transketolase and of the variant E418A from Saccharomyces cerevisiae.
  FEBS J, 272, 1326-1342.  
14742428 J.L.Chuang, R.M.Wynn, C.C.Moss, J.L.Song, J.Li, N.Awad, H.Mandel, and D.T.Chuang (2004).
Structural and biochemical basis for novel mutations in homozygous Israeli maple syrup urine disease patients: a proposed mechanism for the thiamin-responsive phenotype.
  J Biol Chem, 279, 17792-17800.  
15166214 J.Li, R.M.Wynn, M.Machius, J.L.Chuang, S.Karthikeyan, D.R.Tomchick, and D.T.Chuang (2004).
Cross-talk between thiamin diphosphate binding and phosphorylation loop conformation in human branched-chain alpha-keto acid decarboxylase/dehydrogenase.
  J Biol Chem, 279, 32968-32978.
PDB codes: 1v11 1v16 1v1m 1v1r
15514159 R.A.Frank, C.M.Titman, J.V.Pratap, B.F.Luisi, and R.N.Perham (2004).
A molecular switch and proton wire synchronize the active sites in thiamine enzymes.
  Science, 306, 872-876.
PDB codes: 1w85 1w88
15576032 R.M.Wynn, M.Kato, M.Machius, J.L.Chuang, J.Li, D.R.Tomchick, and D.T.Chuang (2004).
Molecular mechanism for regulation of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex by phosphorylation.
  Structure, 12, 2185-2196.
PDB codes: 1u5b 1x7w 1x7x 1x7y 1x7z 1x80
12651851 E.M.Ciszak, L.G.Korotchkina, P.M.Dominiak, S.Sidhu, and M.S.Patel (2003).
Structural basis for flip-flop action of thiamin pyrophosphate-dependent enzymes revealed by human pyruvate dehydrogenase.
  J Biol Chem, 278, 21240-21246.
PDB code: 1ni4
12431983 J.L.Song, J.Li, Y.S.Huang, and D.T.Chuang (2003).
Encapsulation of an 86-kDa assembly intermediate inside the cavities of GroEL and its single-ring variant SR1 by GroES.
  J Biol Chem, 278, 2515-2521.  
12603319 M.Fries, H.J.Chauhan, G.J.Domingo, H.I.Jung, and R.N.Perham (2003).
Site-directed mutagenesis of a loop at the active site of E1 (alpha2beta2) of the pyruvate dehydrogenase complex. A possible common sequence motif.
  Eur J Biochem, 270, 861-870.  
12902323 R.M.Wynn, M.Machius, J.L.Chuang, J.Li, D.R.Tomchick, and D.T.Chuang (2003).
Roles of His291-alpha and His146-beta' in the reductive acylation reaction catalyzed by human branched-chain alpha-ketoacid dehydrogenase: refined phosphorylation loop structure in the active site.
  J Biol Chem, 278, 43402-43410.
PDB codes: 1ols 1olu 1olx
12411477 J.L.Milne, D.Shi, P.B.Rosenthal, J.S.Sunshine, G.J.Domingo, X.Wu, B.R.Brooks, R.N.Perham, R.Henderson, and S.Subramaniam (2002).
Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine.
  EMBO J, 21, 5587-5598.  
11422387 C.Y.Huang, A.K.Chang, P.F.Nixon, and R.G.Duggleby (2001).
Site-directed mutagenesis of the ionizable groups in the active site of Zymomonas mobilis pyruvate decarboxylase: effect on activity and pH dependence.
  Eur J Biochem, 268, 3558-3565.  
11223534 E.Ciszak, L.G.Korotchkina, Y.S.Hong, A.Joachimiak, and M.S.Patel (2001).
Crystallization and initial X-ray diffraction analysis of human pyruvate dehydrogenase.
  Acta Crystallogr D Biol Crystallogr, 57, 465-468.  
  11507102 J.L.Song, and D.T.Chuang (2001).
Natural osmolyte trimethylamine N-oxide corrects assembly defects of mutant branched-chain alpha-ketoacid decarboxylase in maple syrup urine disease.
  J Biol Chem, 276, 40241-40246.  
11509994 L.Edelmann, M.P.Wasserstein, R.Kornreich, C.Sansaricq, S.E.Snyderman, and G.A.Diaz (2001).
Maple syrup urine disease: identification and carrier-frequency determination of a novel founder mutation in the Ashkenazi Jewish population.
  Am J Hum Genet, 69, 863-868.  
  11435118 L.J.Baker, J.A.Dorocke, R.A.Harris, and D.E.Timm (2001).
The crystal structure of yeast thiamin pyrophosphokinase.
  Structure, 9, 539-546.
PDB code: 1ig0
11112664 M.M.Nellis, and D.J.Danner (2001).
Gene preference in maple syrup urine disease.
  Am J Hum Genet, 68, 232-237.  
11583990 N.Nemeria, Y.Yan, Z.Zhang, A.M.Brown, P.Arjunan, W.Furey, J.R.Guest, and F.Jordan (2001).
Inhibition of the Escherichia coli pyruvate dehydrogenase complex E1 subunit and its tyrosine 177 variants by thiamin 2-thiazolone and thiamin 2-thiothiazolone diphosphates. Evidence for reversible tight-binding inhibition.
  J Biol Chem, 276, 45969-45978.  
11526332 S.S.Pang, L.W.Guddat, and R.G.Duggleby (2001).
Crystallization of the catalytic subunit of Saccharomyces cerevisiae acetohydroxyacid synthase.
  Acta Crystallogr D Biol Crystallogr, 57, 1321-1323.  
11106427 H.J.Chauhan, G.J.Domingo, H.I.Jung, and R.N.Perham (2000).
Sites of limited proteolysis in the pyruvate decarboxylase component of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus and their role in catalysis.
  Eur J Biochem, 267, 7158-7169.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.