Rv2454c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: 2-oxoglutarate ferredoxin oxidoreductase subunit beta
- REFSEQ: 2-oxoglutarate ferredoxin oxidoreductase subunit beta
- PATRIC: 2-oxoglutarate oxidoreductase beta subunit (EC 1.2.7.3)
- TUBERCULIST: Probable oxidoreductase (beta subunit)
- NCBI: Probable oxidoreductase (beta subunit)
- updated information (H37Rv4):
  - gene name: korB
  - function: ?-ketoglutarate:ferredoxin oxidoreductase
  - reference: Baughn (2009) PMID: 19936047
Type: Essential
Start: 2753625
End: 2754746
Operon:

Trans-membrane region:
Role: I.B.7 - Miscellaneous oxidoreductases and oxygenases
GO terms:
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0047553 - 2-oxoglutarate synthase activity (Uniprot)
- GO:0030976 - thiamine pyrophosphate binding (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0006099 - tricarboxylic acid cycle (Uniprot)
- GO:0005829 - cytosol (Uniprot)
- GO:0005618 - cell wall (Uniprot)
- GO:0003824 - catalytic activity (Uniprot)
- GO:0000287 - magnesium ion binding (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- COA[c] + AKG[c] + FERI[c] -> CO2[c] + SUCCOA[c] + FERO[c]
Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
Orthologs among selected mycobacteria
Protein structure:
Search for Homologs in PDB

Top 10 Homologs in PDB (as of Nov 2020):

PDB	aa ident	species	PDB title
6N2O	46%	Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1)	2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marinus with 2-oxoglutarate, coenzyme A and succinyl-CoA bound
6N2N	46%	Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1)	Crystal structure of 2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marinus
5B47	45%	Sulfolobus tokodaii str. 7	2-Oxoacid:Ferredoxin Oxidoreductase 2 from Sulfolobus tokodai - pyruvate complex
5B46	45%	Sulfolobus tokodaii str. 7	2-Oxoacid:Ferredoxin Oxidoreductase 2 from Sulfolobus tokodai - ligand free form
5B48	43%	Sulfolobus tokodaii str. 7	2-Oxoacid:Ferredoxin Oxidoreductase 1 from Sulfolobus tokodai

Links to additional information on Rv2454c:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -0.642 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MTRSGDEAQLMTGVTGDLAGTELGLTPSLTKNAGVPTTDQPQKGKDFTSDQEVRWCPGCGDYVILNTIRNFLPELGLRRENIVFISGIGCSSRFPYYLET
YGFHSIHGRAPAIATGLALAREDLSVWVVTGDGDALSIGGNHLIHALRRNINVTILLFNNRIYGLTKGQYSPTSEVGKVTKSTPMGSLDHPFNPVSLALG
AEATFVGRALDSDRNGLTEVLRAAAQHRGAALVEILQDCPIFNDGSFDALRKEGAEERVIKVRHGEPIVFGANGEYCVVKSGFGLEVAKTADVAIDEIIV
HDAQVDDPAYAFALSRLSDQNLDHTVLGIFRHISRPTYDDAARSQVVAARNAAPSGTAALQSLLHGRDTWTVD

(Nucleotide sequence available on KEGG)

Additional Information

Baughn et al (2009). PLOS Pathogens.
An Anaerobic-Type alpha-ketoglutarate Ferredoxin Oxidoreductase Completes the Oxidative Tricarboxylic Acid Cycle of Mycobacterium tuberculosis.
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1000662

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across >100 conditions *new*

Classification	Condition	Strain	Method	Reference	Notes
Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.999850; 15 non-insertions in a row out of 15 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 15 non-insertions in a row out of 15 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 15 non-insertions in a row out of 15 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 15 non-insertions in a row out of 15 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.999950; 15 non-insertions in a row out of 15 sites
No-Data	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Too-Short	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: -1
Growth-Defect	7H09/7H10 + rich media	H37RvMA	MotifHMM	DeJesus et al. (2017)	Fully saturated (14 reps).

TnSeq Data No data currently available.

No TnSeq data currently available for this Target.

RNASeq Data No data currently available.

No RNA-Seq data currently available for this Target.

Metabolomic Profiles No data currently available.

No Metabolomic data currently available for this Target.

Proteomic Data No data currently available.

No Proteomic data currently available for this Target.

Regulatory Relationships from Systems Biology

BioCyc

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

NOTE: Green edges represent the connected genes being classified as differentially essential as a result of the middle gene being knocked out. These interactions are inferred based on RNASeq.

Interactions based on ChIPSeq data

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv3223c (sigH)

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0324 (-) (Upstream of operon)

Interactions based on TFOE data (Rustad et al. 2014)

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv3223c (sigH)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Citation	Central carbon metabolism in Mycobacterium tuberculosis: an unexpected frontier. authors,KY. Rhee,LP. de Carvalho,R. Bryk,S. Ehrt,J. Marrero,SW. Park,D. Schnappinger,A. Venugopal,C. Nathan Trends Microbiol. 2011	extern:JZUCKER		21561773	Traceable author statement to experimental support
Term	EC:1.2.7.3 2-oxoglutarate synthase. - NR	extern:JZUCKER	NR		Traceable author statement to experimental support authors,KY. Rhee,LP. de Carvalho,R. Bryk,S. Ehrt,J. Marrero,SW. Park,D. Schnappinger,A. Venugopal,C. Nathan Central carbon metabolism in Mycobacterium tuberculosis: an unexpected frontier. Trends Microbiol. 2011
Citation	An anaerobic-type alpha-ketoglutarate ferredoxin oxidoreductase completes the oxidative tricarboxylic acid cycle of Mycobacterium tuberculosis. AD. Baughn, SJ. Garforth et al. PLoS Pathog. 2009	extern:JZUCKER		19936047	Inferred from mutant phenotype
Term	EC:1.2.7.3 2-oxoglutarate synthase. - NR	extern:JZUCKER	NR		Inferred from mutant phenotype AD. Baughn, SJ. Garforth et al. An anaerobic-type alpha-ketoglutarate ferredoxin oxidoreductase completes the oxidative tricarboxylic acid cycle of Mycobacterium tuberculosis. PLoS Pathog. 2009

TB Genome Annotation Portal