PDBsum entry 6i2s

Oxidoreductase

PDB id

6i2s

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Contents

			Protein chains

					830 a.a.


					97 a.a.

			Ligands

					PO4


					TD6

			Metals

					_MG


					_CA

			Waters ×159

PDB id:

6i2s

Links

Name:

Oxidoreductase

Title:

Crystal structure of the suca domain of mycobacterium smegmatis kgd (r802a) in complex with gara, following 2-oxoglutarate soak

Structure:

Multifunctional 2-oxoglutarate metabolism enzyme. Chain: a. 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. Mutation: yes. Glycogen accumulation regulator gara.

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. Gene: gara, msmeg_3647, msmei_3561. Expression_system_taxid: 469008

Resolution:

2.40Å

R-factor:

0.193

R-free:

0.219

Authors:

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

Key ref:

T.Wagner et al. (2019). Structural insights into the functional versatility o fha domain protein in mycobacterial signaling.. Sci signal, 12, . PubMed id: 31064884

Date:

01-Nov-18

Release date:

22-May-19

PROCHECK

	Headers

	References

Protein chain

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

Seq: Struc:

Seq: Struc:

Seq: Struc:					1227 a.a. 830 a.a.*

Protein chain

A0QYG2 (GARA_MYCS2) - Glycogen accumulation regulator GarA from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)

Seq: Struc:					158 a.a. 97 a.a.

Key:

Secondary structure

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



		Enzyme reactions

Enzyme class 2:

Chain A: E.C.1.2.4.2 - oxoglutarate dehydrogenase (succinyl-transferring).

[IntEnz] [ExPASy] [KEGG] [BRENDA]

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	+	H(+)	=	N(6)-[(R)- S(8)-succinyldihydrolipoyl]-L-lysyl-[protein]	+	CO2

Cofactor:

Thiamine diphosphate

Thiamine diphosphate
Bound ligand (Het Group name = TD6) matches with 78.79% similarity

Enzyme class 3:

Chain A: E.C.2.2.1.5 - 2-hydroxy-3-oxoadipate synthase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Pathway:

Reaction:

glyoxylate + 2-oxoglutarate + H⁺ = 2-hydroxy-3-oxoadipate + CO2

glyoxylate	+	2-oxoglutarate	+	H(+)	=	2-hydroxy-3-oxoadipate	+	CO2

Cofactor:

Thiamine diphosphate

Thiamine diphosphate
Bound ligand (Het Group name = TD6) matches with 78.79% similarity

Enzyme class 4:

Chain A: E.C.2.3.1.61 - dihydrolipoyllysine-residue succinyltransferase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Pathway:

Reaction:

N₆-[(R)-dihydrolipoyl]-L-lysyl-[protein] + succinyl-CoA = N₆-[(R)- S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CoA

N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein]	+	succinyl-CoA	=	N(6)-[(R)- S(8)-succinyldihydrolipoyl]-L-lysyl-[protein]	+	CoA

Enzyme class 5:

Chain A: E.C.4.1.1.71 - 2-oxoglutarate decarboxylase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

2-oxoglutarate + H⁺ = succinate semialdehyde + CO2

2-oxoglutarate	+	H(+)	=	succinate semialdehyde	+	CO2

Cofactor:

Thiamine diphosphate

Thiamine diphosphate
Bound ligand (Het Group name = TD6) matches with 78.79% similarity

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