PDBsum entry 1ni4

Oxidoreductase

PDB id: 1ni4

Contents

Protein chains

362 a.a. *

330 a.a. *

Ligands

TPP ×2

Metals

__K ×2

_MG ×2

Waters ×742

* Residue conservation analysis

PDB id:

1ni4

Name:

Oxidoreductase

Title:

Human pyruvate dehydrogenase

Structure:

Pyruvate dehydrogenase e1 component: alpha subunit. Chain: a, c. Synonym: pdhe1-a type i. Engineered: yes. Pyruvate dehydrogenase e1 component: beta subunit. Chain: b, d. Synonym: pdhe1-b. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.95Å R-factor: 0.202 R-free: 0.244

Authors:

E.Ciszak,L.G.Korotchkina,P.M.Dominiak,S.Sidhu,M.S.Patel

Key ref:

E.M.Ciszak et al. (2003). Structural basis for flip-flop action of thiamin pyrophosphate-dependent enzymes revealed by human pyruvate dehydrogenase. J Biol Chem, 278, 21240-21246. PubMed id: 12651851 DOI: 10.1074/jbc.M300339200

Date:

20-Dec-02 Release date: 17-Jun-03

Protein chains

P08559  (ODPA_HUMAN) -  Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial from Homo sapiens

Seq: 390 a.a.

Struc: 362 a.a.*

Protein chains

P11177  (ODPB_HUMAN) -  Pyruvate dehydrogenase E1 component subunit beta, mitochondrial from Homo sapiens

Seq: 359 a.a.

Struc: 330 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.1.2.4.1 - pyruvate dehydrogenase (acetyl-transferring).
• Pathway: Oxo-acid dehydrogenase complexes
• Reaction: N₆-[(R)-lipoyl]-L-lysyl-[protein] + pyruvate + H⁺ = N₆-[(R)-S(8)- acetyldihydrolipoyl]-L-lysyl-[protein] + CO2
• Cofactor: Thiamine diphosphate

Thiamine diphosphate (Bound ligand (Het Group name = TPP) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M300339200

J Biol Chem 278:21240-21246 (2003)

PubMed id: 12651851

Structural basis for flip-flop action of thiamin pyrophosphate-dependent enzymes revealed by human pyruvate dehydrogenase.

E.M.Ciszak, L.G.Korotchkina, P.M.Dominiak, S.Sidhu, M.S.Patel.

ABSTRACT

The derivative of vitamin B1, thiamin pyrophosphate, is a cofactor of enzymes performing catalysis in pathways of energy production. In alpha2beta2-heterotetrameric human pyruvate dehydrogenase, this cofactor is used to cleave the Calpha-C(=O) bond of pyruvate followed by reductive acetyl transfer to lipoyl-dihydrolipoamide acetyltransferase. The dynamic nonequivalence of two, otherwise chemically equivalent, catalytic sites has not yet been understood. To understand the mechanism of action of this enzyme, we determined the crystal structure of the holo-form of human pyruvate dehydrogenase at 1.95-A resolution. We propose a model for the flip-flop action of this enzyme through a concerted approximately 2-A shuttle-like motion of its heterodimers. Similarity of thiamin pyrophosphate binding in human pyruvate dehydrogenase with functionally related enzymes suggests that this newly defined shuttle-like motion of domains is common to the family of thiamin pyrophosphate-dependent enzymes.

Selected figure(s)

Figure 2.
FIG. 2. Structure of human pyruvate dehydrogenase (E1p). The four subunits are arranged tetrahedrally as shown in the following colors: , red; ', green; , yellow; and ', blue. The molecule possesses a 2-fold symmetry axis that relates the with the ' subunit and with the ' subunit. Two cofactor molecules, TPP, are shown in black. Two Mg2+ ions, each at the pyrophosphate terminus of TPP, are shown as spheres in dark blue. The two K+ ions contained in the structure are represented as magenta spheres. The locations of six domains termed PP, PP', PYR, PYR', C, and C' domains distributed along the alpha and beta subunits are indicated by arrows. This figure was prepared using PyMol (33).

Figure 3.
FIG. 3. K+ binding site in E1p. The metal binding at this site stabilizes the negative end of the helix (160-165) in the PYR domain of the subunit that forms interactions with the C terminus of the subunit (340-343 and 361). The coordination of K+ is maintained by four carbonyl oxygen atoms, three from Ala^160, Asp163, Asn165, and one from Ile^112. There, coordination is completed by the water molecule W10 to form geometry of a distorted tetragonal pyramid. Similar contacts are observed between the second K+ ion and the symmetry-related ' and ' subunits.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 21240-21246) copyright 2003.

Figures were selected by an automated process.