PDBsum entry 1y8o

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
Protein chains
374 a.a. *
97 a.a. *
__K ×2
Waters ×67
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of the pdk3-l2 complex
Structure: [Pyruvate dehydrogenase [lipoamide]] kinase isozy chain: a. Synonym: pyruvate dehydrogenase kinase isoform 3. Engineered: yes. Dihydrolipoyllysine-residue acetyltransferase com pyruvate dehydrogenase complex. Chain: b. Synonym: e2, dihydrolipoamide acetyltransferase component o dehydrogenase complex, pdc-e2, 70 kda mitochondrial autoant
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: pdk3. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Gene: dlat, dlta.
Biol. unit: Tetramer (from PDB file)
2.48Å     R-factor:   0.211     R-free:   0.234
Authors: M.Kato,J.L.Chuang,R.M.Wynn,D.T.Chuang
Key ref:
M.Kato et al. (2005). Crystal structure of pyruvate dehydrogenase kinase 3 bound to lipoyl domain 2 of human pyruvate dehydrogenase complex. EMBO J, 24, 1763-1774. PubMed id: 15861126 DOI: 10.1038/sj.emboj.7600663
13-Dec-04     Release date:   24-May-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q15120  (PDK3_HUMAN) -  [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrial
406 a.a.
374 a.a.
Protein chain
Pfam   ArchSchema ?
P10515  (ODP2_HUMAN) -  Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
647 a.a.
97 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: Chain A: E.C.  - [Pyruvate dehydrogenase (acetyl-transferring)] kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + [pyruvate dehydrogenase (acetyl-transferring)] = ADP + [pyruvate dehydrogenase (acetyl-transferring)] phosphate
+ [pyruvate dehydrogenase (acetyl-transferring)]
Bound ligand (Het Group name = ADP)
corresponds exactly
+ [pyruvate dehydrogenase (acetyl-transferring)] phosphate
   Enzyme class 3: Chain B: E.C.  - Dihydrolipoyllysine-residue acetyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Reaction: Acetyl-CoA + enzyme N6-(dihydrolipoyl)lysine = CoA + enzyme N6- (S-acetyldihydrolipoyl)lysine
enzyme N(6)-(dihydrolipoyl)lysine
Bound ligand (Het Group name = RED)
matches with 84.62% similarity
Bound ligand (Het Group name = ADP)
matches with 56.25% similarity
+ enzyme N(6)- (S-acetyldihydrolipoyl)lysine
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrion   2 terms 
  Biological process     peroxisome proliferator activated receptor signaling pathway   14 terms 
  Biochemical function     nucleotide binding     8 terms  


DOI no: 10.1038/sj.emboj.7600663 EMBO J 24:1763-1774 (2005)
PubMed id: 15861126  
Crystal structure of pyruvate dehydrogenase kinase 3 bound to lipoyl domain 2 of human pyruvate dehydrogenase complex.
M.Kato, J.L.Chuang, S.C.Tso, R.M.Wynn, D.T.Chuang.
The human pyruvate dehydrogenase complex (PDC) is regulated by reversible phosphorylation by four isoforms of pyruvate dehydrogenase kinase (PDK). PDKs phosphorylate serine residues in the dehydrogenase (E1p) component of PDC, but their amino-acid sequences are unrelated to eukaryotic Ser/Thr/Tyr protein kinases. PDK3 binds to the inner lipoyl domains (L2) from the 60-meric transacetylase (E2p) core of PDC, with concomitant stimulated kinase activity. Here, we present crystal structures of the PDK3-L2 complex with and without bound ADP or ATP. These structures disclose that the C-terminal tail from one subunit of PDK3 dimer constitutes an integral part of the lipoyl-binding pocket in the N-terminal domain of the opposing subunit. The two swapped C-terminal tails promote conformational changes in active-site clefts of both PDK3 subunits, resulting in largely disordered ATP lids in the ADP-bound form. Our structural and biochemical data suggest that L2 binding stimulates PDK3 activity by disrupting the ATP lid, which otherwise traps ADP, to remove product inhibition exerted by this nucleotide. We hypothesize that this allosteric mechanism accounts, in part, for E2p-augmented PDK3 activity.
  Selected figure(s)  
Figure 4.
Figure 4 Interaction surfaces between PDK3 and L2. Interfaces between PDK3 and L2 are shown in molecular surface representations. L2 is separated from PDK3 and rotated by 180 to show the binding interfaces on both proteins. (A) A single L2 binds to the N-terminal domain of PDK3 subunit I. The corresponding interfaces are in green. (B) The C-terminal tail of PDK3 subunit I binds to L2' in complex with subunit II (cf. Figure 2A). Binding surfaces between the tail and L2' are in navy blue. (C) The electrostatic potential surfaces of PDK3 and L2 were calculated with APBS based on the Poisson -Boltzmann equation (Baker et al, 2001). Positive-charged regions are shown in blue, and negative-charged regions in red. The interfaces between the N-terminal domain of PDK3 and L2 (cf. A) consist of hydrophobic interactions in the lipoyl-binding pocket and its surrounding regions as well as electrostatic interactions on the lower portion of the N-terminal domain. Conserved residues in human PDKs and the lipoyl domains of human PDC are indicated.
Figure 5.
Figure 5 Structure of the hydrophobic lipoyl-binding pocket in PDK3. The lipoyl-binding pocket is formed by a loop region between helices 1 (not shown) and 2, as well as helices 2, 3, and 8. These regions form a cylindrical pocket containing conserved hydrophobic residues (brown). The lipoyl-lysine residue (yellow) projects into the hydrophobic pocket. The final 2F[o]-F[c] electron density (blue, contoured at 1 ) is superimposed on the lipoyl-lysine residue. The inset shows a different view of the bound reduced dihydrolipoamide. The C-terminal tail (red) from the other PDK3 subunit is integrated into the lipoyl-binding pocket. The first and last residue numbers of the C-terminal tail are indicated.
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2005, 24, 1763-1774) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19240034 C.A.Brautigam, R.M.Wynn, J.L.Chuang, and D.T.Chuang (2009).
Subunit and catalytic component stoichiometries of an in vitro reconstituted human pyruvate dehydrogenase complex.
  J Biol Chem, 284, 13086-13098.  
19833728 J.Li, M.Kato, and D.T.Chuang (2009).
Pivotal role of the C-terminal DW-motif in mediating inhibition of pyruvate dehydrogenase kinase 2 by dichloroacetate.
  J Biol Chem, 284, 34458-34467.  
18627174 A.Klyuyeva, A.Tuganova, and K.M.Popov (2008).
Allosteric coupling in pyruvate dehydrogenase kinase 2.
  Biochemistry, 47, 8358-8366.  
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
18658136 R.M.Wynn, M.Kato, J.L.Chuang, S.C.Tso, J.Li, and D.T.Chuang (2008).
Pyruvate dehydrogenase kinase-4 structures reveal a metastable open conformation fostering robust core-free basal activity.
  J Biol Chem, 283, 25305-25315.
PDB codes: 2zkj 3d2r
18387944 T.Green, A.Grigorian, A.Klyuyeva, A.Tuganova, M.Luo, and K.M.Popov (2008).
Structural and functional insights into the molecular mechanisms responsible for the regulation of pyruvate dehydrogenase kinase 2.
  J Biol Chem, 283, 15789-15798.
PDB codes: 3crk 3crl
17154432 A.K.Hirsch, F.R.Fischer, and F.Diederich (2007).
Phosphate recognition in structural biology.
  Angew Chem Int Ed Engl, 46, 338-352.  
17544412 A.Klyuyeva, A.Tuganova, and K.M.Popov (2007).
Amino acid residues responsible for the recognition of dichloroacetate by pyruvate dehydrogenase kinase 2.
  FEBS Lett, 581, 2988-2992.  
17602666 A.Tuganova, A.Klyuyeva, and K.M.Popov (2007).
Recognition of the inner lipoyl-bearing domain of dihydrolipoyl transacetylase and of the blood glucose-lowering compound AZD7545 by pyruvate dehydrogenase kinase 2.
  Biochemistry, 46, 8592-8602.  
17532339 D.G.Vassylyev, and J.Symersky (2007).
Crystal structure of pyruvate dehydrogenase phosphatase 1 and its functional implications.
  J Mol Biol, 370, 417-426.
PDB code: 2pnq
17683942 M.Kato, J.Li, J.L.Chuang, and D.T.Chuang (2007).
Distinct structural mechanisms for inhibition of pyruvate dehydrogenase kinase isoforms by AZD7545, dichloroacetate, and radicicol.
  Structure, 15, 992.
PDB codes: 2q8f 2q8g 2q8h 2q8i
17532006 Y.Devedjiev, C.N.Steussy, and D.G.Vassylyev (2007).
Crystal structure of an asymmetric complex of pyruvate dehydrogenase kinase 3 with lipoyl domain 2 and its biological implications.
  J Mol Biol, 370, 407-416.
PDB code: 2pnr
16267046 E.Di Cera (2006).
A structural perspective on enzymes activated by monovalent cations.
  J Biol Chem, 281, 1305-1308.  
17132539 M.C.Sugden, and M.J.Holness (2006).
Mechanisms underlying regulation of the expression and activities of the mammalian pyruvate dehydrogenase kinases.
  Arch Physiol Biochem, 112, 139-149.  
16849321 S.C.Tso, M.Kato, J.L.Chuang, and D.T.Chuang (2006).
Structural determinants for cross-talk between pyruvate dehydrogenase kinase 3 and lipoyl domain 2 of the human pyruvate dehydrogenase complex.
  J Biol Chem, 281, 27197-27204.  
16517984 Y.Hiromasa, L.Hu, and T.E.Roche (2006).
Ligand-induced effects on pyruvate dehydrogenase kinase isoform 2.
  J Biol Chem, 281, 12568-12579.  
16216081 A.Klyuyeva, A.Tuganova, and K.M.Popov (2005).
The carboxy-terminal tail of pyruvate dehydrogenase kinase 2 is required for the kinase activity.
  Biochemistry, 44, 13573-13582.  
16093239 K.R.Rajashankar, R.Bryk, R.Kniewel, J.A.Buglino, C.F.Nathan, and C.D.Lima (2005).
Crystal structure and functional analysis of lipoamide dehydrogenase from Mycobacterium tuberculosis.
  J Biol Chem, 280, 33977-33983.
PDB code: 2a8x
16164760 M.Parsons, E.A.Worthey, P.N.Ward, and J.C.Mottram (2005).
Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi.
  BMC Genomics, 6, 127.  
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.