Rv2476c (gdh)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: glutamate dehydrogenase
- REFSEQ: NAD-dependent glutamate dehydrogenase
- PATRIC: NAD-specific glutamate dehydrogenase (EC 1.4.1.2) large form
- TUBERCULIST: Probable NAD-dependent glutamate dehydrogenase Gdh (NAD-Gdh) (NAD-dependent glutamic dehydrogenase)
- NCBI: Probable NAD-dependent glutamate dehydrogenase Gdh (NAD-Gdh) (NAD-dependent glutamic dehydrogenase)
- updated information (H37Rv4):
  - gene name: gdh
  - function:
  - reference:
Type: Not Target
Start: 2777388
End: 2782262
Operon:

Trans-membrane region:
Role: VI - Unknowns
GO terms:
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0019551 - glutamate catabolic process to 2-oxoglutarate (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005829 - cytosol (Uniprot)
- GO:0005618 - cell wall (Uniprot)
- GO:0005515 - protein binding (Uniprot)
- GO:0004352 - glutamate dehydrogenase (NAD+) activity (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- NADPH[c] + AKG[c] + NH3[c] <=> NADP[c] + GLU[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): (none with >35% aa id)
Links to additional information on gdh:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.414 (from Jeremy Rock's lab)
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology
- KEGG - nucleotide and amino acid sequences of gene

Amino Acid Sequence

MTIDPGAKQDVEAWTTFTASADIPDWISKAYIDSYRGPRDDSSEATKAAEASWLPASLLTPAMLGAHYRLGRHRAAGESCVAVYRADDPAGFGPALQVVA
EHGGMLMDSVTVLLHRLGIAYAAILTPVFDVHRSPTGELLRIEPKAEGTSPHLGEAWMHVALSPAVDHKGLAEVERLLPKVLADVQRVATDATALIATLS
ELAGEVESNAGGRFSAPDRQDVGELLRWLGDGNFLLLGYQRCRVADGMVYGEGSSGMGVLRGRTGSRPRLTDDDKLLVLAQARVGSYLRYGAYPYAIAVR
EYVDGSVVEHRFVGLFSVAAMNADVLEIPTISRRVREALAMAESDPSHPGQLLLDVIQTVPRPELFTLSAQRLLTMARAVVDLGSQRQALLFLRADRLQY
FVSCLVYMPRDRYTTAVRMQFEDILVREFGGTRLEFTARVSESPWALMHFMVRLPEVGVAGEGAAAPPVDVSEANRIRIQGLLTEAARTWADRLIGAAAA
AGSVGQADAMHYAAAFSEAYKQAVTPADAIGDIAVITELTDDSVKLVFSERDEQGVAQLTWFLGGRTASLSQLLPMLQSMGVVVLEERPFSVTRPDGLPV
WIYQFKISPHPTIPLAPTVAERAATAHRFAEAVTAIWHGRVEIDRFNELVMRAGLTWQQVVLLRAYAKYLRQAGFPYSQSYIESVLNEHPATVRSLVDLF
EALFVPVPSGSASNRDAQAAAAAVAADIDALVSLDTDRILRAFASLVQATLRTNYFVTRQGSARCRDVLALKLNAQLIDELPLPRPRYEIFVYSPRVEGV
HLRFGPVARGGLRWSDRRDDFRTEILGLVKAQAVKNAVIVPVGAKGGFVVKRPPLPTGDPAADRDATRAEGVACYQLFISGLLDVTDNVDHATASVNPPP
EVVRRDGDDAYLVVAADKGTATFSDIANDVAKSYGFWLGDAFASGGSVGYDHKAMGITARGAWEAVKRHFREIGIDTQTQDFTVVGIGDMSGDVFGNGML
LSKHIRLIAAFDHRHIFLDPNPDAAVSWAERRRMFELPRSSWSDYDRSLISEGGGVYSREQKAIPLSAQVRAVLGIDGSVDGGAAEMAPPNLIRAILRAP
VDLLFNGGIGTYIKAESESDADVGDRANDPVRVNANQVRAKVIGEGGNLGVTALGRVEFDLSGGRINTDALDNSAGVDCSDHEVNIKILIDSLVSAGTVK
ADERTQLLESMTDEVAQLVLADNEDQNDLMGTSRANAASLLPVHAMQIKYLVAERGVNRELEALPSEKEIARRSEAGIGLTSPELATLMAHVKLGLKEEV
LATELPDQDVFASRLPRYFPTALRERFTPEIRSHQLRREIVTTMLINDLVDTAGITYAFRIAEDVGVTPIDAVRTYVATDAIFGVGHIWRRIRAANLPIA
LSDRLTLDTRRLIDRAGRWLLNYRPQPLAVGAEINRFAAMVKALTPRMSEWLRGDDKAIVEKTAAEFASQGVPEDLAYRVSTGLYRYSLLDIIDIADIAD
IDAAEVADTYFALMDRLGTDGLLTAVSQLPRHDRWHSLARLAIRDDIYGALRSLCFDVLAVGEPGESSEQKIAEWEHLSASRVARARRTLDDIRASGQKD
LATLSVAARQIRRMTRTSGRGISG

(Nucleotide sequence available on KEGG)

Additional Information

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: 0.994700; 15 non-insertions in a row out of 64 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 34 non-insertions in a row out of 64 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 16 non-insertions in a row out of 64 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 36 non-insertions in a row out of 64 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 45 non-insertions in a row out of 64 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
Non-Essential	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:
- Rv0818 (-)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings to other targets were found.

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Not upregulated by other genes.
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0818 (-)

Property	Value	Creator	Evidence	PMID	Comment
Citation	Glutamate synthesis in Streptomyces coelicolor. authors,SH. Fisher J. Bacteriol. 1989	jjmcfadden		2708309	Inferred from direct assay
Term	EC:1.4.1.4 Glutamate dehydrogenase (NADP(+)). - NR	jjmcfadden	NR		Inferred from direct assay authors,SH. Fisher Glutamate synthesis in Streptomyces coelicolor. J. Bacteriol. 1989

TB Genome Annotation Portal