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PDBsum entry 1lab
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Transferase (acyltransferase) PDB id
1lab

 

 

 

 

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Contents
Protein chain
80 a.a. *
* Residue conservation analysis
PDB id:
1lab
Name: Transferase (acyltransferase)
Title: Three-dimensional structure of the lipoyl domain from bacillus stearothermophilus pyruvate dehydrogenase multienzyme complex
Structure: Dihydrolipoamide acetyltransferase. Chain: a. Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: bacillus stearothermophilus.
NMR struc: 11 models
Authors: F.Dardel,A.L.Davis,E.D.Laue,R.N.Perham
Key ref: F.Dardel et al. (1993). Three-dimensional structure of the lipoyl domain from Bacillus stearothermophilus pyruvate dehydrogenase multienzyme complex. J Mol Biol, 229, 1037-1048. PubMed id: 8445635
Date:
02-Sep-92     Release date:   15-Jul-93    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11961  (ODP2_GEOSE) -  Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex from Geobacillus stearothermophilus
Seq:
Struc: 		428 a.a.
80 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.1.12  - dihydrolipoyllysine-residue acetyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Oxo-acid dehydrogenase complexes
      Reaction: N6-[(R)-dihydrolipoyl]-L-lysyl-[protein] + acetyl-CoA = N6-[(R)-S(8)- acetyldihydrolipoyl]-L-lysyl-[protein] + CoA
N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein]
 + acetyl-CoA
 = N(6)-[(R)-S(8)- acetyldihydrolipoyl]-L-lysyl-[protein]
 + CoA
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
J Mol Biol 229:1037-1048 (1993)
PubMed id: 8445635  
 
 
Three-dimensional structure of the lipoyl domain from Bacillus stearothermophilus pyruvate dehydrogenase multienzyme complex.
F.Dardel, A.L.Davis, E.D.Laue, R.N.Perham.
 
  ABSTRACT  
 
The structure of the lipoyl domain from the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus has been determined by means of nuclear magnetic resonance spectroscopy. A total of 452 nuclear Overhauser effect distance constraints and 76 dihedral angle restraints were employed as the input for the structure calculations, which were performed using a hybrid distance geometry-simulated annealing strategy and the programs DISGEO and X-PLOR. The overall structure of the lipoyl domain (residues 1 to 79 of the dihydrolipoamide acetyltransferase polypeptide chain) is that of a flattened eight-stranded beta-barrel folded around a core of well-defined hydrophobic residues. The lipoylation site, lysine 42, is located in the middle of a beta-turn, and the N and C-terminal residues of the domain are close together in adjacent beta-strands at the opposite end of the molecule. The polypeptide backbone exhibits a 2-fold axis of quasi-symmetry, with the C alpha atoms of residues 15 to 39 and 52 to 76 being almost superimposable on those of residues 52 to 76 and 15 to 39, respectively (root-mean-square deviation = 1.48 A). The amino acid residues at key positions in the structure are conserved among all the reported primary structures of lipoyl domains, suggesting that the domains all fold in a similar way.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20361979 S.Vijayakrishnan, S.M.Kelly, R.J.Gilbert, P.Callow, D.Bhella, T.Forsyth, J.G.Lindsay, and O.Byron (2010).
Solution structure and characterisation of the human pyruvate dehydrogenase complex core assembly.
  J Mol Biol, 399, 71-93.  
19863063 S.Puthenveetil, D.S.Liu, K.A.White, S.Thompson, and A.Y.Ting (2009).
Yeast display evolution of a kinetically efficient 13-amino acid substrate for lipoic acid ligase.
  J Am Chem Soc, 131, 16430-16438.  
18372281 B.Bagautdinov, Y.Matsuura, S.Bagautdinova, and N.Kunishima (2008).
Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate.
  J Biol Chem, 283, 14739-14750.
PDB codes: 1x01 2d5d 2dxu 2dzc 2e41 2e64 2ejf 2ejg 2evb 2zgw
18184587 J.S.Lengyel, K.M.Stott, X.Wu, B.R.Brooks, A.Balbo, P.Schuck, R.N.Perham, S.Subramaniam, and J.L.Milne (2008).
Extended polypeptide linkers establish the spatial architecture of a pyruvate dehydrogenase multienzyme complex.
  Structure, 16, 93.  
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.  
16861235 C.F.Chang, H.T.Chou, Y.J.Lin, S.J.Lee, J.L.Chuang, D.T.Chuang, and T.H.Huang (2006).
Structure of the subunit binding domain and dynamics of the di-domain region from the core of human branched chain alpha-ketoacid dehydrogenase complex.
  J Biol Chem, 281, 28345-28353.  
16263718 E.M.Ciszak, A.Makal, Y.S.Hong, A.K.Vettaikkorumakankauv, L.G.Korotchkina, and M.S.Patel (2006).
How dihydrolipoamide dehydrogenase-binding protein binds dihydrolipoamide dehydrogenase in the human pyruvate dehydrogenase complex.
  J Biol Chem, 281, 648-655.
PDB code: 1zy8
16699181 G.Cui, B.Nan, J.Hu, Y.Wang, C.Jin, and B.Xia (2006).
Identification and solution structures of a single domain biotin/lipoyl attachment protein from Bacillus subtilis.
  J Biol Chem, 281, 20598-20607.
PDB code: 1z6h
16308322 J.L.Milne, X.Wu, M.J.Borgnia, J.S.Lengyel, B.R.Brooks, D.Shi, R.N.Perham, and S.Subramaniam (2006).
Molecular structure of a 9-MDa icosahedral pyruvate dehydrogenase subcomplex containing the E2 and E3 enzymes using cryoelectron microscopy.
  J Biol Chem, 281, 4364-4370.  
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
14622277 H.I.Jung, A.Cooper, and R.N.Perham (2003).
Interactions of the peripheral subunit-binding domain of the dihydrolipoyl acetyltransferase component in the assembly of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus.
  Eur J Biochem, 270, 4488-4496.  
12756305 Y.Gu, Z.H.Zhou, D.B.McCarthy, L.J.Reed, and J.K.Stoops (2003).
3D electron microscopy reveals the variable deposition and protein dynamics of the peripheral pyruvate dehydrogenase component about the core.
  Proc Natl Acad Sci U S A, 100, 7015-7020.  
12044183 A.F.Hengeveld, C.P.van Mierlo, H.W.van den Hooven, A.J.Visser, and A.de Kok (2002).
Functional and structural characterization of a synthetic peptide representing the N-terminal domain of prokaryotic pyruvate dehydrogenase.
  Biochemistry, 41, 7490-7500.  
11839747 C.F.Chang, H.T.Chou, J.L.Chuang, D.T.Chuang, and T.H.Huang (2002).
Solution structure and dynamics of the lipoic acid-bearing domain of human mitochondrial branched-chain alpha-keto acid dehydrogenase complex.
  J Biol Chem, 277, 15865-15873.
PDB codes: 1k8m 1k8o
12003954 C.Wanner, and J.Soppa (2002).
Functional role for a 2-oxo acid dehydrogenase in the halophilic archaeon Haloferax volcanii.
  J Bacteriol, 184, 3114-3121.  
11956202 J.E.Cronan (2002).
Interchangeable enzyme modules. Functional replacement of the essential linker of the biotinylated subunit of acetyl-CoA carboxylase with a linker from the lipoylated subunit of pyruvate dehydrogenase.
  J Biol Chem, 277, 22520-22527.  
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.  
11559360 K.Tozawa, R.W.Broadhurst, A.R.Raine, C.Fuller, A.Alvarez, G.Guillen, G.Padron, and R.N.Perham (2001).
Solution structure of the lipoyl domain of the chimeric dihydrolipoyl dehydrogenase P64K from Neisseria meningitidis.
  Eur J Biochem, 268, 4908-4917.
PDB code: 1gjx
11752427 Z.H.Zhou, D.B.McCarthy, C.M.O'Connor, L.J.Reed, and J.K.Stoops (2001).
The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes.
  Proc Natl Acad Sci U S A, 98, 14802-14807.  
10913250 D.D.Jones, K.M.Stott, M.J.Howard, and R.N.Perham (2000).
Restricted motion of the lipoyl-lysine swinging arm in the pyruvate dehydrogenase complex of Escherichia coli.
  Biochemistry, 39, 8448-8459.
PDB code: 1qjo
  10739245 J.E.Knapp, D.Carroll, J.E.Lawson, S.R.Ernst, L.J.Reed, and M.L.Hackert (2000).
Expression, purification, and structural analysis of the trimeric form of the catalytic domain of the Escherichia coli dihydrolipoamide succinyltransferase.
  Protein Sci, 9, 37-48.
PDB code: 1c4t
10806400 K.Koike, T.Suematsu, and M.Ehara (2000).
Cloning, overexpression and mutagenesis of cDNA encoding dihydrolipoamide succinyltransferase component of the porcine 2-oxoglutarate dehydrogenase complex.
  Eur J Biochem, 267, 3005-3016.  
10806385 M.Neuburger, A.M.Polidori, E.Piètre, M.Faure, A.Jourdain, J.Bourguignon, B.Pucci, and R.Douce (2000).
Interaction between the lipoamide-containing H-protein and the lipoamide dehydrogenase (L-protein) of the glycine decarboxylase multienzyme system. 1. Biochemical studies.
  Eur J Biochem, 267, 2882-2889.  
10966480 R.N.Perham (2000).
Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions.
  Annu Rev Biochem, 69, 961.  
10788482 X.Gong, T.Peng, A.Yakhnin, M.Zolkiewski, J.Quinn, S.J.Yeaman, and T.E.Roche (2000).
Specificity determinants for the pyruvate dehydrogenase component reaction mapped with mutated and prosthetic group modified lipoyl domains.
  J Biol Chem, 275, 13645-13653.  
9880519 A.Chapman-Smith, T.W.Morris, J.C.Wallace, and J.E.Cronan (1999).
Molecular recognition in a post-translational modification of exceptional specificity. Mutants of the biotinylated domain of acetyl-CoA carboxylase defective in recognition by biotin protein ligase.
  J Biol Chem, 274, 1449-1457.  
10518807 A.F.Hengeveld, S.E.Schoustra, A.H.Westphal, and A.de Kok (1999).
Pyruvate dehydrogenase from Azotobacter vinelandii. Properties of the N-terminally truncated enzyme.
  Eur J Biochem, 265, 1098-1107.  
10213607 E.L.Roberts, N.Shu, M.J.Howard, R.W.Broadhurst, A.Chapman-Smith, J.C.Wallace, T.Morris, J.E.Cronan, and R.N.Perham (1999).
Solution structures of apo and holo biotinyl domains from acetyl coenzyme A carboxylase of Escherichia coli determined by triple-resonance nuclear magnetic resonance spectroscopy.
  Biochemistry, 38, 5045-5053.
PDB codes: 2bdo 3bdo
10329614 P.Reche, and R.N.Perham (1999).
Structure and selectivity in post-translational modification: attaching the biotinyl-lysine and lipoyl-lysine swinging arms in multifunctional enzymes.
  EMBO J, 18, 2673-2682.  
9655933 A.de Kok, A.F.Hengeveld, A.Martin, and A.H.Westphal (1998).
The pyruvate dehydrogenase multi-enzyme complex from Gram-negative bacteria.
  Biochim Biophys Acta, 1385, 353-366.  
  9792103 D.V.Reddy, S.Rothemund, B.C.Shenoy, P.R.Carey, and F.D.Sönnichsen (1998).
Structural characterization of the entire 1.3S subunit of transcarboxylase from Propionibacterium shermanii.
  Protein Sci, 7, 2156-2163.  
  9649469 M.J.Howard, C.Fuller, R.W.Broadhurst, R.N.Perham, J.G.Tang, J.Quinn, A.G.Diamond, and S.J.Yeaman (1998).
Three-dimensional structure of the major autoantigen in primary biliary cirrhosis.
  Gastroenterology, 115, 139-146.
PDB code: 1fyc
9119000 A.Berg, J.Vervoort, and A.de Kok (1997).
Three-dimensional structure in solution of the N-terminal lipoyl domain of the pyruvate dehydrogenase complex from Azotobacter vinelandii.
  Eur J Biochem, 244, 352-360.
PDB codes: 1iyu 1iyv
9325338 A.Chapman-Smith, B.E.Forbes, J.C.Wallace, and J.E.Cronan (1997).
Covalent modification of an exposed surface turn alters the global conformation of the biotin carrier domain of Escherichia coli acetyl-CoA carboxylase.
  J Biol Chem, 272, 26017-26022.  
9108146 A.F.Neuwald, J.S.Liu, D.J.Lipman, and C.E.Lawrence (1997).
Extracting protein alignment models from the sequence database.
  Nucleic Acids Res, 25, 1665-1677.  
9241431 C.Chothia, T.Hubbard, S.Brenner, H.Barns, and A.Murzin (1997).
Protein folds in the all-beta and all-alpha classes.
  Annu Rev Biophys Biomol Struct, 26, 597-627.  
9045657 D.Yang, J.Song, T.Wagenknecht, and T.E.Roche (1997).
Assembly and full functionality of recombinantly expressed dihydrolipoyl acetyltransferase component of the human pyruvate dehydrogenase complex.
  J Biol Chem, 272, 6361-6369.  
  9278137 J.Alcedo, and M.Noll (1997).
Hedgehog and its patched-smoothened receptor complex: a novel signalling mechanism at the cell surface.
  Biol Chem, 378, 583-590.  
9398236 X.Yao, D.Wei, C.Soden, M.F.Summers, and D.Beckett (1997).
Structure of the carboxy-terminal fragment of the apo-biotin carboxyl carrier subunit of Escherichia coli acetyl-CoA carboxylase.
  Biochemistry, 36, 15089-15100.
PDB code: 1a6x
8617275 D.Macherel, J.Bourguignon, E.Forest, M.Faure, C.Cohen-Addad, and R.Douce (1996).
Expression, lipoylation and structure determination of recombinant pea H-protein in Escherichia coli.
  Eur J Biochem, 236, 27-33.  
8988025 I.A.Lessard, C.Fuller, and R.N.Perham (1996).
Competitive interaction of component enzymes with the peripheral subunit-binding domain of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus: kinetic analysis using surface plasmon resonance detection.
  Biochemistry, 35, 16863-16870.  
8805537 S.S.Mande, S.Sarfaty, M.D.Allen, R.N.Perham, and W.G.Hol (1996).
Protein-protein interactions in the pyruvate dehydrogenase multienzyme complex: dihydrolipoamide dehydrogenase complexed with the binding domain of dihydrolipoamide acetyltransferase.
  Structure, 4, 277-286.
PDB code: 1ebd
8994880 Y.Lindqvist, and G.Schneider (1996).
Protein-biotin interactions.
  Curr Opin Struct Biol, 6, 798-803.  
8529634 A.Berg, O.Smits, A.de Kok, and J.Vervoort (1995).
Sequential 1H and 15N nuclear magnetic resonance assignments and secondary structure of the lipoyl domain of the 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii. Evidence for high structural similarity with the lipoyl domain of the pyruvate dehydrogenase complex.
  Eur J Biochem, 234, 148-159.  
8575446 A.H.Westphal, A.Fabisz-Kijowska, H.Kester, P.P.Obels, and A.de Kok (1995).
The interaction between lipoamide dehydrogenase and the peripheral-component-binding domain from the Azotobacter vinelandii pyruvate dehydrogenase complex.
  Eur J Biochem, 234, 861-870.  
7719855 C.Cohen-Addad, S.Pares, L.Sieker, M.Neuburger, and R.Douce (1995).
The lipoamide arm in the glycine decarboxylase complex is not freely swinging.
  Nat Struct Biol, 2, 63-68.
PDB code: 1htp
8747466 F.K.Athappilly, and W.A.Hendrickson (1995).
Structure of the biotinyl domain of acetyl-coenzyme A carboxylase determined by MAD phasing.
  Structure, 3, 1407-1419.
PDB code: 1bdo
7567952 R.Bringas, and J.Fernandez (1995).
A lipoamide dehydrogenase from Neisseria meningitidis has a lipoyl domain.
  Proteins, 21, 303-306.  
8068086 A.Berg, A.de Kok, and J.Vervoort (1994).
Sequential 1H and 15N nuclear magnetic resonance assignments and secondary structure of the N-terminal lipoyl domain of the dihydrolipoyl transacetylase component of the pyruvate dehydrogenase complex from Azotobacter vinelandii.
  Eur J Biochem, 221, 87.  
8051937 F.Peinemann, and D.J.Danner (1994).
Maple syrup urine disease 1954 to 1993.
  J Inherit Metab Dis, 17, 3.  
8197146 S.Pares, C.Cohen-Addad, L.Sieker, M.Neuburger, and R.Douce (1994).
X-ray structure determination at 2.6-A resolution of a lipoate-containing protein: the H-protein of the glycine decarboxylase complex from pea leaves.
  Proc Natl Acad Sci U S A, 91, 4850-4853.  
8081735 C.Chothia, and A.G.Murzin (1993).
New folds for all-beta proteins.
  Structure, 1, 217-222.  
  8518734 S.M.Brocklehurst, and R.N.Perham (1993).
Prediction of the three-dimensional structures of the biotinylated domain from yeast pyruvate carboxylase and of the lipoylated H-protein from the pea leaf glycine cleavage system: a new automated method for the prediction of protein tertiary structure.
  Protein Sci, 2, 626-639.  
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.

 

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