Rv3250c (rubB)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: rubredoxin-2
- REFSEQ: rubredoxin RubB
- PATRIC: Rubredoxin
- TUBERCULIST: Probable rubredoxin RubB
- NCBI: Probable rubredoxin RubB
- updated information (H37Rv4):
  - gene name: rubB
  - function:
  - reference:
Type: Not Target
Start: 3630384
End: 3630566
Operon:

Trans-membrane region:
Role: I.B.6.c - Electron transport
GO terms:
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0046872 - metal ion binding (Uniprot)
- GO:0005506 - iron ion binding (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
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: 2kn9
Search for Homologs in PDB

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

PDB	aa ident	species	PDB title
2KN9	98%	Mycobacterium tuberculosis	Solution structure of zinc-substituted rubredoxin B (Rv3250c) from Mycobacterium tuberculosis. Seattle Structural Genomics Center for Infectious Disease target MytuD.01635.a
2V3B	66%	PSEUDOMONAS AERUGINOSA	Crystal structure of the electron transfer complex rubredoxin - rubredoxin reductase from Pseudomonas aeruginosa.
1S24	56%	Pseudomonas oleovorans	Rubredoxin domain II from Pseudomonas oleovorans
1YK4	56%	Pyrococcus abyssi	Ultra-high resolution structure of Pyrococcus abyssi rubredoxin W4L/R5S
2M4Y	56%	Mycobacterium ulcerans	Rubredoxin type protein from Mycobacterium ulcerans
1YK5	56%	Pyrococcus abyssi	Pyrococcus abyssi rubredoxin
5OME	54%	Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)	The cryofrozen atomic resolution X-ray crystal structure of the reduced form (Fe2+) perdeuterated Pyrococcus furiosus Rubredoxin in D2O (100K, 0.75 Angstrom resolution)
5NW3	54%	Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)	The cryofrozen atomic resolution X-ray crystal structure of perdeuterated Pyrococcus furiosus Rubredoxin (100K, 0.59A resolution)
5AI3	54%	PYROCOCCUS FURIOSUS	X-ray structure of 113Cd-substituted Perdeuterated Pyrococcus furiosus rubredoxin to 1.02A resolution at 295K in a quartz capillary
5AI2	54%	PYROCOCCUS FURIOSUS	Anomalous Neutron phased crystal structure of 113Cd-substituted Perdeuterated Pyrococcus furiosus rubredoxin to 1.75A resolution at 295K

Links to additional information on rubB:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.681 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VNDYKLFRCIQCGFEYDEALGWPEDGIAAGTRWDDIPDDWSCPDCGAAKSDFEMVEVARS

(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
Too-Short	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 0 non-insertions in a row out of 3 sites
Too-Short	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 0 non-insertions in a row out of 3 sites
Too-Short	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 0 non-insertions in a row out of 3 sites
Too-Short	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: -1.000000; 0 non-insertions in a row out of 3 sites
Too-Short	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: -1.000000; 0 non-insertions in a row out of 3 sites
Non-Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Non-Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 2.6
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:
- Rv0273c (-)
- Rv3286c (sigF)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0047c (-) (Direct binding)
- Rv0081 (-) (Direct binding)
- Rv0678 (-) (Direct binding)
- Rv3765c (tcrX) (Direct binding)
- Rv0023 (-) (Upstream of operon)
- Rv1033c (trcR) (Upstream of operon)
- Rv1255c (-) (Upstream of operon)
- Rv1985c (-) (Upstream of operon)
- Rv3249c (-) (Upstream of operon)
- Rv3488 (-) (Upstream of operon)
- Rv3597c (lsr2) (Upstream of operon)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv3286c (sigF)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0273c (-)

Property	Value	Creator	Evidence	PMID	Comment
Citation	The genes rubA and rubB for alkane degradation in Acinetobacter sp. strain ADP1 are in an operon with estB, encoding an esterase, and oxyR. authors,W. Geissdrfer,RG. Kok,A. Ratajczak,KJ. Hellingwerf,W. Hillen J. Bacteriol. 1999	priti.priety	ISA	10400587	Operon (Functional linkage)
Interaction	Transcription Rv3251c	priti.priety	ISA		Operon (Functional linkage) authors,W. Geissdrfer,RG. Kok,A. Ratajczak,KJ. Hellingwerf,W. Hillen The genes rubA and rubB for alkane degradation in Acinetobacter sp. strain ADP1 are in an operon with estB, encoding an esterase, and oxyR. J. Bacteriol. 1999
Interaction	Transcription Rv3251c	priti.priety	ISA		Operon (Functional linkage) authors,W. Geissdrfer,RG. Kok,A. Ratajczak,KJ. Hellingwerf,W. Hillen The genes rubA and rubB for alkane degradation in Acinetobacter sp. strain ADP1 are in an operon with estB, encoding an esterase, and oxyR. J. Bacteriol. 1999
Interaction	RegulatedBy Rv3681c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	RegulatedBy Rv1956	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	RegulatedBy Rv1359	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	RegulatedBy Rv0818	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	RegulatedBy Rv0491	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Citation	Rubredoxins involved in alkane oxidation. authors,JB. van Beilen,M. Neuenschwander,TH. Smits,C. Roth,SB. Balada,B. Witholt J. Bacteriol. 2002	extern:JZUCKER		11872724	Assay of protein purified to homogeneity from a heterlogous host
Term	EC:1.14.15.3 Alkane 1-monooxygenase. - NR	extern:JZUCKER	NR		Assay of protein purified to homogeneity from a heterlogous host authors,JB. van Beilen,M. Neuenschwander,TH. Smits,C. Roth,SB. Balada,B. Witholt Rubredoxins involved in alkane oxidation. J. Bacteriol. 2002
Citation	Functional analysis of alkane hydroxylases from gram-negative and gram-positive bacteria. TH. Smits, SB. Balada et al. J. Bacteriol. 2002	extern:JZUCKER		11872725	Assay of protein partially-purified from its native host
Term	EC:1.14.15.3 Alkane 1-monooxygenase. - NR	extern:JZUCKER	NR		Assay of protein partially-purified from its native host TH. Smits, SB. Balada et al. Functional analysis of alkane hydroxylases from gram-negative and gram-positive bacteria. J. Bacteriol. 2002

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