PDBsum entry: 2jgd

Oxidoreductase

PDB id: 2jgd

Contents

Protein chains

812 a.a. *

Ligands

AMP ×2

Waters ×735

* Residue conservation analysis

PDB id:

2jgd

Name:

Oxidoreductase

Title:

E. Coli 2-oxoglutarate dehydrogenase (e1o)

Structure:

2-oxoglutarate dehydrogenase e1 component. Chain: a. Synonym: alpha- ketoglutarate dehydrogenase. Engineered: yes. 2-oxoglutarate dehydrogenase e1 component. Chain: b. Synonym: alpha- ketoglutarate dehydrogenase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.6Å R-factor: 0.189 R-free: 0.250

Authors:

R.A.W.Frank,A.J.Price,F.D.Northrop,R.N.Perham,B.F.Luisi

Key ref:

R.A.Frank et al. (2007). Crystal structure of the E1 component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex. J Mol Biol, 368, 639-651. PubMed id: 17367808 DOI: 10.1016/j.jmb.2007.01.080

Date:

12-Feb-07 Release date: 27-Feb-07

Protein chains

P0AFG3  (ODO1_ECOLI) -  2-oxoglutarate dehydrogenase E1 component

Seq: 933 a.a.

Struc: 812 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.2.4.2 - Oxoglutarate dehydrogenase (succinyl-transferring).
• Pathway: Oxo-acid dehydrogenase complexes
• Reaction: 2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO₂
• Cofactor: Thiamine diphosphate

Thiamine diphosphate (Bound ligand (Het Group name = AMP) matches with 40.00% similarity)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytosol (1 term)
• Biological process: metabolic process (4 terms)
• Biochemical function: oxidoreductase activity (4 terms)

reference

DOI no: 10.1016/j.jmb.2007.01.080

J Mol Biol 368:639-651 (2007)

PubMed id: 17367808

Crystal structure of the E1 component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex.

R.A.Frank, A.J.Price, F.D.Northrop, R.N.Perham, B.F.Luisi.

ABSTRACT

The thiamine-dependent E1o component (EC 1.2.4.2) of the 2-oxoglutarate dehydrogenase complex catalyses a rate-limiting step of the tricarboxylic acid cycle (TCA) of aerobically respiring organisms. We describe the crystal structure of Escherichia coli E1o in its apo and holo forms at 2.6 A and 3.5 A resolution, respectively. The structures reveal the characteristic fold that binds thiamine diphosphate and resemble closely the alpha(2)beta(2) hetero-tetrameric E1 components of other 2-oxo acid dehydrogenase complexes, except that in E1o, the alpha and beta subunits are fused as a single polypeptide. The extended segment that links the alpha-like and beta-like domains forms a pocket occupied by AMP, which is recognised specifically. Also distinctive to E1o are N-terminal extensions to the core fold, and which may mediate interactions with other components of the 2-oxoglutarate dehydrogenase multienzyme complex. The active site pocket contains a group of three histidine residues and one serine that appear to confer substrate specificity and the capacity to accommodate the TCA metabolite oxaloacetate. Oxaloacetate inhibits E1o activity at physiological concentrations, and we suggest that the inhibition may allow coordinated activity within the TCA cycle. We discuss the implications for metabolic control in facultative anaerobes, and for energy homeostasis of the mammalian brain.

Selected figure(s)

Figure 3.
Figure 3. Stereo views of the electron density of putative ligands; the map was generated with sigmaA-weighted coefficients and contoured to 1σ. (a) Active site of E1o showing Mg^2+, ThDP and an oxaloacetate molecule bound (yellow sphere, cyan and gold stick format, respectively). This structure represents E1o in an inhibited conformation as oxaloacetate occludes the site where the substrate is expected to bind. The residues mediating the interactions with oxaloacetate are shown in stick format. (b) AMP binding pocket of E1o. Figure 3. Stereo views of the electron density of putative ligands; the map was generated with sigmaA-weighted coefficients and contoured to 1σ. (a) Active site of E1o showing Mg^2+, ThDP and an oxaloacetate molecule bound (yellow sphere, cyan and gold stick format, respectively). This structure represents E1o in an inhibited conformation as oxaloacetate occludes the site where the substrate is expected to bind. The residues mediating the interactions with oxaloacetate are shown in stick format. (b) AMP binding pocket of E1o.

Figure 5.
Figure 5. The AMP binding pocket highlighting key residues that engage the ligand. The interacting residues are shown with a solvent-accessible surface. The adenine ring is base-stacked against the indole ring of Trp533 and the aliphatic portion of Arg710. Hydrogen bonds from the back-bone of residue 711 and 673 specify the adenine form of the purine ring. The phosphate of AMP forms a bidentate salt-bridge with Arg337, a water-mediated H-bond with Arg710, and H-bonds with Ser302 and His313. Two double Ala mutants were engineered to disrupt interactions with the adenine ring (*) and the phosphate (†) of AMP. Figure 5. The AMP binding pocket highlighting key residues that engage the ligand. The interacting residues are shown with a solvent-accessible surface. The adenine ring is base-stacked against the indole ring of Trp533 and the aliphatic portion of Arg710. Hydrogen bonds from the back-bone of residue 711 and 673 specify the adenine form of the purine ring. The phosphate of AMP forms a bidentate salt-bridge with Arg337, a water-mediated H-bond with Arg710, and H-bonds with Ser302 and His313. Two double Ala mutants were engineered to disrupt interactions with the adenine ring (*) and the phosphate (†) of AMP.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 368, 639-651) copyright 2007.

Figures were selected by an automated process.