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PDBsum entry 1v1r

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1v1r
Jmol
Contents
Protein chains
352 a.a. *
336 a.a. *
Ligands
SO4
GOL ×2
Metals
_CL ×3
__K ×2
_NA ×2
Waters ×531
* Residue conservation analysis
PDB id:
1v1r
Name: Oxidoreductase
Title: Crosstalk between cofactor binding and the phosphorylation loop conformation in the bckd machine
Structure: 2-oxoisovalerate dehydrogenase alpha subunit. Chain: a. Synonym: mitochondrial precursor, branched-chain alpha-keto dehydrogenase e1, component alpha chain, bckdh e1-alpha, b engineered: yes. 2-oxoisovalerate dehydrogenase beta subunit. Chain: b. Synonym: mitochondrial precursor, branched-chain alpha-keto dehydrogenase e1, component beta chain, bckdh e1-beta.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Groes. Other_details: expression system used bl-21 cells with overexpressing groel and groes
Biol. unit: Tetramer (from PDB file)
Resolution:
1.80Å     R-factor:   0.158     R-free:   0.183
Authors: J.Li,R.M.Wynn,M.Machius,J.L.Chuang,S.Karthikeyan,D.R.Tomchic D.T.Chuang
Key ref:
J.Li et al. (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. PubMed id: 15166214 DOI: 10.1074/jbc.M403611200
Date:
22-Apr-04     Release date:   03-Jun-04    
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.
352 a.a.
Protein chain
Pfam   ArchSchema ?
P21953  (ODBB_HUMAN) -  2-oxoisovalerate dehydrogenase subunit beta, mitochondrial
Seq:
Struc:
392 a.a.
336 a.a.
Key:    PfamA 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
Bound ligand (Het Group name = GOL)
matches with 55.56% similarity
+ [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine
= [dihydrolipoyllysine- residue (2-methylpropanoyl)transferase] S-(2-methylpropanoyl)dihydrolipoyllysine
+ CO(2)
      Cofactor: Thiamine diphosphate
Thiamine diphosphate
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   8 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M403611200 J Biol Chem 279:32968-32978 (2004)
PubMed id: 15166214  
 
 
Cross-talk between thiamin diphosphate binding and phosphorylation loop conformation in human branched-chain alpha-keto acid decarboxylase/dehydrogenase.
J.Li, R.M.Wynn, M.Machius, J.L.Chuang, S.Karthikeyan, D.R.Tomchick, D.T.Chuang.
 
  ABSTRACT  
 
The decarboxylase/dehydrogenase (E1b) component of the 4-megadalton human branched-chain alpha-keto acid dehydrogenase (BCKD) metabolic machine is a thiamin diphosphate (ThDP)-dependent enzyme with a heterotetrameric cofactor-binding fold. The E1b component catalyzes the decarboxylation of alpha-keto acids and the subsequent reductive acylation of the lipoic acid-bearing domain (LBD) from the 24-meric transacylase (E2b) core. In the present study, we show that the binding of cofactor ThDP to the E1b active site induces a disorder-to-order transition of the conserved phosphorylation loop carrying the two phosphorylation sites Ser(292)-alpha and Ser(302)-alpha, as deduced from the 1.80-1.85 A apoE1b and holoE1b structures. The induced loop conformation is essential for the recognition of lipoylated LBD to initiate E1b-catalyzed reductive acylation. Alterations of invariant Arg(287)-alpha, Asp(295)-alpha, Tyr(300)-alpha, and Arg(301)-alpha that form a hydrogen-bonding network in the phosphorylation loop result in the disordering of the loop conformation as elucidated by limited proteolysis, accompanied by the impaired binding and diminished reductive acylation of lipoylated LBD. In contrast, k(cat) values for E1b-catalyzed decarboxylation of the alpha-keto acid are higher in these E1b mutants than in wild-type E1b, with higher K(m) values for the substrate in the mutants. ThDP binding that orders the loop prevents phosphorylation of E1b by the BCKD kinase and averts the inactivation of wild-type E1b, but not the above mutants, by this covalent modification. Our results establish that the cross-talk between the bound ThDP and the phosphorylation loop conformation serves as a feed-forward switch for multiple reaction steps in the BCKD metabolic machine.
 
  Selected figure(s)  
 
Figure 3.
FIG. 3. Substitutions of residues participating in the hydrogen-bonding network result in markedly decreased reductive acylation (Reaction 3) activity. Invariant residues (Arg287- , Asp295- , Tyr300- , and Arg301- ) that form the hydrogen-bonding network were changed to alanine or phenylalanine in the case of Tyr300- . Reductive acylation of lip-LBD catalyzed by wild-type or mutant E1b was measured with [U-14C]KIV as a substrate as described under "Experimental Procedures." Activity for reductive acylation is expressed as percent relative to the wild type (2.3 min-1). The nonspecific radioactivity incorporated into nonlipoylated LBD and the wild-type or mutant E1b protein served as a blank. Results are averages of two independent experiments.
Figure 7.
FIG. 7. ThDP inhibits the phosphorylation of wild-type but not mutant E1b. A, the reaction mixture contained human apoE1b protein, lipoylated E2b, and maltose-binding protein-tagged rat BCKD kinase in the absence and presence of increasing ThDP concentrations. The phosphorylation reaction was initiated by adding 0.4 mM [ -32P]ATP and was incubated at 25 °C for 1 min. The reaction mixtures were separated by SDS-PAGE. 32P incorporation into the subunit of E1b proteins was quantified by PhosphorImaging. The PhosphorImage counts in wild-type and each mutant E1b in the absence of ThDP was set as 100% with respect to the corresponding E1b protein. B, PhosphorImaging of 32P incorporation into the subunit of the S302A- E1b mutant and E1b double mutants containing the S302A- mutation and a second mutation in the hydrogen-bonding network. The phosphorylation was carried out in the absence of ThDP.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 32968-32978) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21098507 N.Brunetti-Pierri, B.Lanpher, A.Erez, E.A.Ananieva, M.Islam, J.C.Marini, Q.Sun, C.Yu, M.Hegde, J.Li, R.M.Wynn, D.T.Chuang, S.Hutson, and B.Lee (2011).
Phenylbutyrate therapy for maple syrup urine disease.
  Hum Mol Genet, 20, 631-640.  
19858196 M.M.Islam, M.Nautiyal, R.M.Wynn, J.A.Mobley, D.T.Chuang, and S.M.Hutson (2010).
Branched-chain amino acid metabolon: interaction of glutamate dehydrogenase with the mitochondrial branched-chain aminotransferase (BCATm).
  J Biol Chem, 285, 265-276.  
20099870 X.Y.Pei, K.M.Erixon, B.F.Luisi, and F.J.Leeper (2010).
Structural insights into the prereaction state of pyruvate decarboxylase from Zymomonas mobilis .
  Biochemistry, 49, 1727-1736.
PDB codes: 2wva 2wvg 2wvh
19801660 S.Kale, and F.Jordan (2009).
Conformational ensemble modulates cooperativity in the rate-determining catalytic step in the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex.
  J Biol Chem, 284, 33122-33129.  
19081061 M.Kato, R.M.Wynn, J.L.Chuang, S.C.Tso, M.Machius, J.Li, and D.T.Chuang (2008).
Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops.
  Structure, 16, 1849-1859.
PDB codes: 3exe 3exf 3exg 3exh 3exi
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.  
16579849 G.E.Homanics, K.Skvorak, C.Ferguson, S.Watkins, and H.S.Paul (2006).
Production and characterization of murine models of classic and intermediate maple syrup urine disease.
  BMC Med Genet, 7, 33.  
16954186 J.Stetefeld, M.Jenny, and P.Burkhard (2006).
Intersubunit signaling in glutamate-1-semialdehyde-aminomutase.
  Proc Natl Acad Sci U S A, 103, 13688-13693.
PDB codes: 2hoy 2hoz 2hp1 2hp2
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
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 codes are shown on the right.