Rv3552 (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: CoA-transferase beta subunit
- REFSEQ: CoA-transferase subunit beta
- PATRIC: Putative CoA-transferase subunit beta Rv3552/MT3656 (EC 2.8.3.-)
- TUBERCULIST: Possible CoA-transferase (beta subunit)
- NCBI: Possible CoA-transferase (beta subunit)
- updated information (H37Rv4):
  - gene name: ipdB
  - function:
  - reference: (Crowe 2018, PMID: 29581275) (Wilburn, 2018; PMID: 29718271)
Type: Conditional
Start: 3990771
End: 3991523
Operon:

Trans-membrane region:
Role: VI - Unknowns
GO terms:
- GO:0044117 - growth of symbiont in host (Uniprot)
- GO:0016740 - transferase activity (Uniprot)
- GO:0008410 - CoA-transferase activity (Uniprot)
- GO:0008152 - metabolic process (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:
Search for Homologs in PDB

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

PDB	aa ident	species	PDB title
6CON	99%	Mycobacterium tuberculosis	Crystal structure of Mycobacterium tuberculosis IpdAB
6COJ	69%	Rhodococcus jostii	Crystal structure of Rhodococcus jostii RHA1 IpdAB E105A COCHEA-COA complex
6CO9	69%	Rhodococcus jostii	Crystal structure of Rhodococcus jostii RHA1 IpdAB COCHEA-COA complex
6CO6	69%	Rhodococcus jostii (strain RHA1)	Crystal structure of Rhodococcus jostii RHA1 IpdAB

Links to additional information on Rv3552:
- Mycobrowser
- PATRIC
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.582 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- BioCyc
- Systems Biology

Amino Acid Sequence

VSTRAEVCAVACAELFRDAGEIMISPMTNMASVGARLARLTFAPDILLTDGEAQLLADTPALGKTGAPNRIEGWMPFGRVFETLAWGRRHVVMGANQVDR
YGNQNISAFGPLQRPTRQMFGVRGSPGNTINHATSYWVGNHCKRVFVEAVDVVSGIGYDKVDPDNPAFRFVNVYRVVSNLGVFDFGGPDHSMRAVSLHPG
VTPGDVRDATSFEVHDLDAAEQTRLPTDDELHLIRAVIDPKSLRDREIRS

(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
Non-Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 10 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 10 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 10 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 10 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.998800; 10 non-insertions in a row out of 10 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:

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv3557c (-) (Upstream of operon)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0260c (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:

Property	Value	Creator	Evidence	PMID	Comment
Interaction	RegulatedBy Rv3416	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 Rv3334	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 Rv2175c	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 Rv1931c	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 Rv0823c	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 Rv0445c	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	Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages. authors,J. Rengarajan,BR. Bloom,EJ. Rubin Proc. Natl. Acad. Sci. U.S.A. 2005	nsampson		15928073	Reaction blocked in mutant
Term	EC:6.2.1.3 Long-chain-fatty-acid--CoA ligase. - NR	nsampson	NR		Reaction blocked in mutant authors,J. Rengarajan,BR. Bloom,EJ. Rubin Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages. Proc. Natl. Acad. Sci. U.S.A. 2005

TB Genome Annotation Portal