PDBsum entry 1ik6

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protein links
Oxidoreductase PDB id
Protein chain
284 a.a. *
Waters ×134
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: 3d structure of the e1beta subunit of pyruvate dehydrogenase from the archeon pyrobaculum aerophilum
Structure: Pyruvate dehydrogenase. Chain: a. Fragment: e1beta subunit. Engineered: yes
Source: Pyrobaculum aerophilum. Organism_taxid: 13773. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PDB file)
2.00Å     R-factor:   0.212     R-free:   0.255
Authors: G.Kleiger,J.Perry,D.Eisenberg
Key ref:
G.Kleiger et al. (2001). 3D structure and significance of the GPhiXXG helix packing motif in tetramers of the E1beta subunit of pyruvate dehydrogenase from the archeon Pyrobaculum aerophilum. Biochemistry, 40, 14484-14492. PubMed id: 11724561 DOI: 10.1021/bi011016k
02-May-01     Release date:   19-Dec-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q8ZUR7  (Q8ZUR7_PYRAE) -  Pyruvate dehydrogenase E1 beta subunit
320 a.a.
284 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     1 term  


DOI no: 10.1021/bi011016k Biochemistry 40:14484-14492 (2001)
PubMed id: 11724561  
3D structure and significance of the GPhiXXG helix packing motif in tetramers of the E1beta subunit of pyruvate dehydrogenase from the archeon Pyrobaculum aerophilum.
G.Kleiger, J.Perry, D.Eisenberg.
As part of a structural genomics project, we have determined the 2.0 A structure of the E1beta subunit of pyruvate dehydrogenase from Pyrobaculum aerophilum (PA), a thermophilic archaeon. The overall fold of E1beta from PA is closely similar to the previously determined E1beta structures from humans (HU) and P. putida (PP). However, unlike the HU and PP structures, the PA structure was determined in the absence of its partner subunit, E1alpha. Significant structural rearrangements occur in E1beta when its E1alpha partner is absent, including rearrangement of several secondary structure elements such as helix C. Helix C is buried by E1alpha in the HU and PP structures, but makes crystal contacts in the PA structure that lead to an apparent beta(4) tetramer. Static light scattering and sedimentation velocity data are consistent with the formation of PA E1beta tetramers in solution. The interaction of helix C with its symmetry-related counterpart stabilizes the tetrameric interface, where two glycine residues on the same face of one helix create a packing surface for the other helix. This GPhiXXG helix-helix interaction motif has previously been found in interacting transmembrane helices, and is found here at the E1alpha-E1beta interface for both the HU and PP alpha(2)beta(2) tetramers. As a case study in structural genomics, this work illustrates that comparative analysis of protein structures can identify the structural significance of a sequence motif.

Literature references that cite this PDB file's key reference

  PubMed id Reference
17635906 L.D.Cabrita, J.A.Irving, M.C.Pearce, J.C.Whisstock, and S.P.Bottomley (2007).
Aeropin from the extremophile Pyrobaculum aerophilum bypasses the serpin misfolding trap.
  J Biol Chem, 282, 26802-26809.  
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.  
15640214 I.Treede, G.Hauser, A.Mühlenweg, C.Hofmann, M.Schmidt, G.Weitnauer, S.Glaser, and A.Bechthold (2005).
Genes involved in formation and attachment of a two-carbon chain as a component of eurekanate, a branched-chain sugar moiety of avilamycin A.
  Appl Environ Microbiol, 71, 400-406.  
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
15313242 A.Senes, D.E.Engel, and W.F.DeGrado (2004).
Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs.
  Curr Opin Struct Biol, 14, 465-479.  
14691237 G.Kleiger, E.M.Panina, P.Mallick, and D.Eisenberg (2004).
PFIT and PFRIT: bioinformatic algorithms for detecting glycosidase function from structure and sequence.
  Protein Sci, 13, 221-229.  
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
12649422 W.F.DeGrado, H.Gratkowski, and J.D.Lear (2003).
How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles.
  Protein Sci, 12, 647-665.  
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.