PDBsum entry 6r2c

Oxidoreductase

PDB id: 6r2c

Contents

Protein chains

814 a.a.

Ligands

TPP ×4

JQ5 ×4

Metals

_MG ×4

_CA ×4

Waters ×847

PDB id:

6r2c

Name:

Oxidoreductase

Title:

Crystal structure of the suca domain of mycobacterium smegmatis kgd after soaking with succinylphosphonate phosphonoethyl ester (pesp)

Structure:

Multifunctional 2-oxoglutarate metabolism enzyme. Chain: a, b, c, d. Synonym: 2-hydroxy-3-oxoadipate synthase,hoas,2-oxoglutarate carboxy- lyase,2-oxoglutarate decarboxylase,alpha-ketoglutarate decarboxylase, kgd,alpha-ketoglutarate-glyoxylate carboligase. Ec: 2.2.1.5,4.1.1.71,1.2.4.2,2.3.1.61. Engineered: yes

Source:

Mycobacterium smegmatis (strain atcc 700084 / mc(2)155). Organism_taxid: 246196. Strain: atcc 700084 / mc(2)155. Gene: kgd, suca, msmeg_5049, msmei_4922. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008

Resolution:

2.09Å R-factor: 0.233 R-free: 0.246

Authors:

T.Wagner,P.M.Alzari,M.Bellinzoni

Key ref:

T.Wagner et al. (2019). Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: From a Michaelis-like complex to ThDP adducts. J Struct Biol, 208, 182-190. PubMed id: 31476368 DOI: 10.1016/j.jsb.2019.08.012

Date:

15-Mar-19 Release date: 11-Sep-19

Protein chains

A0R2B1  (KGD_MYCS2) -  Multifunctional 2-oxoglutarate metabolism enzyme from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)

Seq: 1227 a.a.

Struc: 814 a.a.

Enzyme reactions

• Enzyme class 2: E.C.1.2.4.2 - oxoglutarate dehydrogenase (succinyl-transferring).
• Pathway: Oxo-acid dehydrogenase complexes
• Reaction: N₆-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate + H⁺ = N₆-[(R)- S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CO2

N(6)-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate (Bound ligand (Het Group name = JQ5) matches with 43.75% similarity) + H(+) = N(6)-[(R)- S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CO2

• Cofactor: Thiamine diphosphate

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

• Enzyme class 3: E.C.2.2.1.5 - 2-hydroxy-3-oxoadipate synthase.

Pathway:

• Reaction: glyoxylate + 2-oxoglutarate + H⁺ = 2-hydroxy-3-oxoadipate + CO2

glyoxylate (Bound ligand (Het Group name = JQ5) matches with 43.75% similarity) + 2-oxoglutarate + H(+) = 2-hydroxy-3-oxoadipate + CO2

• Cofactor: Thiamine diphosphate

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

• Enzyme class 4: E.C.2.3.1.61 - dihydrolipoyllysine-residue succinyltransferase.

Pathway:

• Reaction: N₆-[(R)-dihydrolipoyl]-L-lysyl-[protein] + succinyl-CoA = N₆-[(R)- S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CoA
• Enzyme class 5: E.C.4.1.1.71 - 2-oxoglutarate decarboxylase.
• Reaction: 2-oxoglutarate + H⁺ = succinate semialdehyde + CO2

2-oxoglutarate + H(+) = succinate semialdehyde + CO2 (Bound ligand (Het Group name = JQ5) matches with 53.85% similarity)

• Cofactor: Thiamine diphosphate

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

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

reference

DOI no: 10.1016/j.jsb.2019.08.012

J Struct Biol 208:182-190 (2019)

PubMed id: 31476368

Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: From a Michaelis-like complex to ThDP adducts.

T.Wagner, A.Boyko, P.M.Alzari, V.I.Bunik, M.Bellinzoni.

ABSTRACT

Mycobacterial KGD, the thiamine diphosphate (ThDP)-dependent E1o component of the 2-oxoglutarate dehydrogenase complex (OGDHC), is known to undergo significant conformational changes during catalysis with two distinct conformational states, previously named as the early and late state. In this work, we employ two phosphonate analogues of 2-oxoglutarate (OG), i.e. succinyl phosphonate (SP) and phosphono ethyl succinyl phosphonate (PESP), as tools to isolate the first catalytic steps and understand the significance of conformational transitions for the enzyme regulation. The kinetics showed a more efficient inhibition of mycobacterial E1o by SP (K_i 0.043 ± 0.013 mM) than PESP (K_i 0.88 ± 0.28 mM), consistent with the different circular dichroism spectra of the corresponding complexes. PESP allowed us to get crystallographic snapshots of the Michaelis-like complex, the first one for 2-oxo acid dehydrogenases, followed by the covalent adduction of the inhibitor to ThDP, mimicking the pre-decarboxylation complex. In addition, covalent ThDP-phosphonate complexes obtained with both compounds by co-crystallization were in the late conformational state, probably corresponding to slowly dissociating enzyme-inhibitor complexes. We discuss the relevance of these findings in terms of regulatory features of the mycobacterial E1o enzymes, and in the perspective of developing tools for species-specific metabolic regulation.