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PDBsum entry 2yid
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PDB id:
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Lyase
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Title:
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Crystal structure of the suca domain of mycobacterium smegmatis alpha- ketoglutarate decarboxylase in complex with the enamine-thdp intermediate
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Structure:
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2-oxoglutarate decarboxylase. Chain: a, b, c, d. Fragment: residues 361-1227. Synonym: 2-oxoglutarate carboxy-lyase, alpha-ketoglutarate decarboxylase, kdh. Engineered: yes
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Source:
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Mycobacterium smegmatis. Organism_taxid: 1772. Strain: mc2155. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: plyss.
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Resolution:
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2.25Å
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R-factor:
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0.194
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R-free:
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0.223
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Authors:
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T.Wagner,M.Bellinzoni,A.M.Wehenkel,H.M.O'Hare,P.M.Alzari
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Key ref:
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T.Wagner
et al.
(2011).
Functional plasticity and allosteric regulation of α-ketoglutarate decarboxylase in central mycobacterial metabolism.
Chem Biol,
18,
1011-1020.
PubMed id:
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Date:
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11-May-11
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Release date:
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15-Jun-11
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PROCHECK
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Headers
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References
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A0R2B1
(KGD_MYCS2) -
Multifunctional 2-oxoglutarate metabolism enzyme from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
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Seq:
Struc:
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1227 a.a.
844 a.a.
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Key: |
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Secondary structure |
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CATH domain |
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Enzyme class 2:
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E.C.1.2.4.2
- oxoglutarate dehydrogenase (succinyl-transferring).
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Pathway:
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Oxo-acid dehydrogenase complexes
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Reaction:
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N6-[(R)-lipoyl]-L-lysyl-[protein] + 2-oxoglutarate + H+ = N6-[(R)- S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CO2
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N(6)-[(R)-lipoyl]-L-lysyl-[protein]
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+
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2-oxoglutarate
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+
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H(+)
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=
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N(6)-[(R)- S(8)-succinyldihydrolipoyl]-L-lysyl-[protein]
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+
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CO2
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Cofactor:
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Thiamine diphosphate
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Thiamine diphosphate
Bound ligand (Het Group name =
TD7)
matches with 78.79% similarity
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Enzyme class 3:
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E.C.2.2.1.5
- 2-hydroxy-3-oxoadipate synthase.
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Pathway:
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Reaction:
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glyoxylate + 2-oxoglutarate + H+ = 2-hydroxy-3-oxoadipate + CO2
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glyoxylate
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+
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2-oxoglutarate
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+
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H(+)
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=
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2-hydroxy-3-oxoadipate
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+
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CO2
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Cofactor:
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Thiamine diphosphate
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Thiamine diphosphate
Bound ligand (Het Group name =
TD7)
matches with 78.79% similarity
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Enzyme class 4:
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E.C.2.3.1.61
- dihydrolipoyllysine-residue succinyltransferase.
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Pathway:
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Reaction:
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N6-[(R)-dihydrolipoyl]-L-lysyl-[protein] + succinyl-CoA = N6-[(R)- S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CoA
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N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein]
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+
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succinyl-CoA
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=
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N(6)-[(R)- S(8)-succinyldihydrolipoyl]-L-lysyl-[protein]
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+
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CoA
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Enzyme class 5:
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E.C.4.1.1.71
- 2-oxoglutarate decarboxylase.
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Reaction:
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2-oxoglutarate + H+ = succinate semialdehyde + CO2
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2-oxoglutarate
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+
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H(+)
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=
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succinate semialdehyde
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+
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CO2
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Cofactor:
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Thiamine diphosphate
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Thiamine diphosphate
Bound ligand (Het Group name =
TD7)
matches with 78.79% similarity
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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.
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Chem Biol
18:1011-1020
(2011)
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PubMed id:
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Functional plasticity and allosteric regulation of α-ketoglutarate decarboxylase in central mycobacterial metabolism.
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T.Wagner,
M.Bellinzoni,
A.Wehenkel,
H.M.O'Hare,
P.M.Alzari.
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ABSTRACT
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