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PDBsum entry 1umb

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1umb
Jmol
Contents
Protein chains
362 a.a. *
323 a.a. *
Ligands
TDP ×2
Metals
_MG ×2
Waters ×1164
* Residue conservation analysis
PDB id:
1umb
Name: Oxidoreductase
Title: Branched-chain 2-oxo acid dehydrogenase (e1) from thermus thermophilus hb8 in holo-form
Structure: 2-oxo acid dehydrogenase alpha subunit. Chain: a, c. Synonym: e1-alpha. Engineered: yes. 2-oxo acid dehydrogenase beta subunit. Chain: b, d. Synonym: e1-beta. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.10Å     R-factor:   0.169     R-free:   0.194
Authors: T.Nakai,N.Nakagawa,N.Maoka,R.Masui,S.Kuramitsu,N.Kamiya, Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
T.Nakai et al. (2004). Ligand-induced conformational changes and a reaction intermediate in branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8, as revealed by X-ray crystallography. J Mol Biol, 337, 1011-1033. PubMed id: 15033367 DOI: 10.1016/j.jmb.2004.02.011
Date:
25-Sep-03     Release date:   30-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q5SLR4  (ODBA_THET8) -  2-oxoisovalerate dehydrogenase subunit alpha
Seq:
Struc:
367 a.a.
362 a.a.
Protein chains
Pfam   ArchSchema ?
Q5SLR3  (ODBB_THET8) -  2-oxoisovalerate dehydrogenase subunit beta
Seq:
Struc:
324 a.a.
323 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: 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!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2004.02.011 J Mol Biol 337:1011-1033 (2004)
PubMed id: 15033367  
 
 
Ligand-induced conformational changes and a reaction intermediate in branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8, as revealed by X-ray crystallography.
T.Nakai, N.Nakagawa, N.Maoka, R.Masui, S.Kuramitsu, N.Kamiya.
 
  ABSTRACT  
 
The alpha(2)beta(2) tetrameric E1 component of the branched-chain 2-oxo acid (BCOA) dehydrogenase multienzyme complex is a thiamin diphosphate (ThDP)-dependent enzyme. E1 catalyzes the decarboxylation of a BCOA concomitant with the formation of the alpha-carbanion/enamine intermediate, 2-(1-hydroxyalkyl)-ThDP, followed by transfer of the 1-hydroxyalkyl group to the distal sulfur atom on the lipoamide of the E2 component. In order to elucidate the catalytic mechanism of E1, the alpha- and beta-subunits of E1 from Thermus thermophilus HB8 have been co-expressed in Escherichia coli, purified and crystallized as a stable complex, and the following crystal structures have been analyzed: the apoenzyme (E1(apo)), the holoenzyme (E1(holo)), E1(holo) in complex with the substrate analogue 4-methylpentanoate (MPA) as an ES complex model, and E1(holo) in complex with 4-methyl-2-oxopentanoate (MOPA) as the alpha-carbanion/enamine intermediate (E1(ceim)). Binding of cofactors to E1(apo) induces a disorder-order transition in two loops adjacent to the active site. Furthermore, upon binding of MPA to E1(holo), the loop comprised of Gly121beta-Gln131beta moves close to the active site and interacts with MPA. The carboxylate group of MPA is recognized mainly by Tyr86beta and N4' of ThDP. The hydrophobic moiety of MPA is recognized by Phe66alpha, Tyr95alpha, Met128alpha and His131alpha. As an intermediate, MOPA is decarboxylated and covalently linked to ThDP, and the conformation of the protein loop is almost the same as in the substrate-free (holoenzyme) form. These results suggest that E1 undergoes an open-closed conformational change upon formation of the ES complex with a BCOA, and the mobile region participates in the recognition of the carboxylate group of the BCOA. ES complex models of E1(holo).MOPA and of E1(ceim).lipoamide built from the above structures suggest that His273alpha and His129beta' are potential proton donors to the carbonyl group of a BCOA and to the proximal sulfur atom on the lipoamide, respectively.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Stereoview of the Tth E1 structure. A, Overall structure of the a[2]b[2] tetramer in the a-carbanion/enamine intermediate; B, a-subunit; C, b-subunit. The orientations in B and C are the same as that in A. Ligand molecules are represented by spheres (orange for Mg2+, yellow for ThDP and green for HMB group) and those in B and C are shown as semi-transparent to clarify inner structures. Disordered regions in E1[apo], which include the STSH motif (see the text and Figure 3D), are shown in magenta. The substrate-binding loop (see the text and Figure 6) that undergoes conformational change upon binding of MPA is shown in cyan. The designation of secondary structures of Tth E1 is according to those of Ppu E1, resulting in the absence of helix 1.
Figure 6.
Figure 6. Conformational changes upon binding of the substrate analogue MPA. Stereoview of the structure around the substrate-binding loop for E1[holo] (A), E1[holo]·MPA (B) and E1[ceim] (C). Carbon atoms of each subunit are colored according to Figure 1A, whereas a and b in residue labels are omitted. Water molecules are shown as red spheres. Broken lines represent hydrogen bonds.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 337, 1011-1033) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
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.  
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.  
19081062 X.Y.Pei, C.M.Titman, R.A.Frank, F.J.Leeper, and B.F.Luisi (2008).
Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multienzyme complex.
  Structure, 16, 1860-1872.
PDB codes: 3duf 3dv0 3dva
17182735 N.Nemeria, S.Chakraborty, A.Baykal, L.G.Korotchkina, M.S.Patel, and F.Jordan (2007).
The 1',4'-iminopyrimidine tautomer of thiamin diphosphate is poised for catalysis in asymmetric active centers on enzymes.
  Proc Natl Acad Sci U S A, 104, 78-82.  
17057342 K.Chandrasekhar, P.Arjunan, M.Sax, N.Nemeria, F.Jordan, and W.Furey (2006).
Active-site changes in the pyruvate dehydrogenase multienzyme complex E1 apoenzyme component from Escherichia coli observed at 2.32 A resolution.
  Acta Crystallogr D Biol Crystallogr, 62, 1382-1386.
PDB code: 2g67
16531404 P.Arjunan, M.Sax, A.Brunskill, K.Chandrasekhar, N.Nemeria, S.Zhang, F.Jordan, and W.Furey (2006).
A thiamin-bound, pre-decarboxylation reaction intermediate analogue in the pyruvate dehydrogenase E1 subunit induces large scale disorder-to-order transformations in the enzyme and reveals novel structural features in the covalently bound adduct.
  J Biol Chem, 281, 15296-15303.
PDB codes: 2g25 2g28
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
16109942 M.E.Schreiner, D.Fiur, J.Holátko, M.Pátek, and B.J.Eikmanns (2005).
E1 enzyme of the pyruvate dehydrogenase complex in Corynebacterium glutamicum: molecular analysis of the gene and phylogenetic aspects.
  J Bacteriol, 187, 6005-6018.  
15802265 N.Nemeria, K.Tittmann, E.Joseph, L.Zhou, M.B.Vazquez-Coll, P.Arjunan, G.Hübner, W.Furey, and F.Jordan (2005).
Glutamate 636 of the Escherichia coli pyruvate dehydrogenase-E1 participates in active center communication and behaves as an engineered acetolactate synthase with unusual stereoselectivity.
  J Biol Chem, 280, 21473-21482.  
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
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
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.