Rv3201c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: DNA helicase II/ATP-dependent DNA helicase PcrA
- REFSEQ: ATP-dependent DNA helicase
- PATRIC: ATP-dependent DNA helicase SCO5184
- TUBERCULIST: Probable ATP-dependent DNA helicase
- NCBI: Probable ATP-dependent DNA helicase
- updated information (H37Rv4):
  - gene name: -
  - function:
  - reference:
Coordinates in H37Rv: 3573731 - 3577036
Gene length: 3306 bp (with stop codon), 1101 aa (without stop codon)
Operon:

Trans-membrane region:
Role: II.A.5 - DNA replication, repair, recombination and restriction/modification
GO terms:
- GO:0090305 - nucleic acid phosphodiester bond hydrolysis (Uniprot)
- GO:0040007 - growth (Uniprot)
- GO:0032508 - DNA duplex unwinding (Uniprot)
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0006974 - cellular response to DNA damage stimulus (Uniprot)
- GO:0006281 - DNA repair (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005576 - extracellular region (Uniprot)
- GO:0005524 - ATP binding (Uniprot)
- GO:0004527 - exonuclease activity (Uniprot)
- GO:0004518 - nuclease activity (Uniprot)
- GO:0004386 - helicase activity (Uniprot)
- GO:0004003 - ATP-dependent DNA helicase activity (Uniprot)
- GO:0003677 - DNA binding (Uniprot)
- GO:0000166 - nucleotide 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:
Search for Latest Homologs in PDB

Top 10 Homologs in PDB (as of Apr 2026):

PDB	aa ident	species	PDB title
6PPU	68%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Cryo-EM structure of AdnAB-AMPPNP-DNA complex
9NP6	68%	Mycolicibacterium smegmatis MC2 155	Cryo-EM structure of AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP and blunt end DNA
7SJR	68%	Mycolicibacterium smegmatis	Cryo-EM structure of AdnA-AdnB(W325A) in complex with DNA and AMPPNP
6PPR	68%	Mycobacterium smegmatis	Cryo-EM structure of AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP and DNA
6PPJ	61%	Mycobacterium smegmatis	Cryo-EM structure of AdnA(D934A)-AdnB(D1014A) in complex with AMPPNP

Links to additional information on Rv3201c:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.629 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MTQTAAPARYSPAELACALGLFPPTAEQAAVIAAPPGPLVVIAGAGAGKTETMAARVVWLVANGYAEPGQVLGLTFTRKAAGQLLRRVRSRLARLAGIGL
GCGDPAACAPVVSTYHAFAGSLLRDYGLLLPLEPDTRLLSETELWQLAFDVVSGYDGVLCTDKSPAAVTSIVVRLWGQLGEHLVDTRALRDTHVELERLV
HALPAGRYQRDRGPSQWLLRMLATQTQRAELVPLLDALGERMHAGKVMDFAMQMASAARLAATSPQVGQDLRRRYRVVLLDEYQDTGHAQRVVLSSLFGG
GVDDGLALTAVGDPIQSIYGWRGASATNLPRFTTDFPLSDGTPAPVLELLTSWRNPPQALRVANGISAEARRRSVAVRALRPRPDAPPGAVRCALLPDVQ
AEREWIADHLRMRYQRAEADGVKPPTAAVLVRRNADAAAIADTLRARGIPAEVVGLAGLLSIPEVAEVVAMLRLVADPTAGAAAMRVLTGPRWRLGARDL
AALWRRALTLSGESPSTASPESIAMAASADADNPCLADAISDPGSAEGYSVAGYGRIGALAGELSALRGRLGHSLPDLVAEVRRVLGVDCEVRASAPVSG
GWAGPEHLDAFADVVAGYAERASARSSEASVAGLLAYLDVAEVVENGLPPAELTVACDRVQVLTVHAAKGLEWQVVAVAHLSRGVFPSTVSRSSWLTDPA
ELPPLLRGDRASAGAHGIPVLDTSAVADRKQLSDKISEHRRLLDRRRVDEERRLLYVAVTRAEDTLLVSGHHWGPTGTKPRGPSEFLCELKDIIDRSAAA
GDPCGVVEQWASAPAGDERNPLCDNAIEAVWPADPLAARRGDVERGAALVAAAMSADLPGSTTDIDHPPRPGDAPWSTDVDALLAERAHAARGAPARGLP
NHLSVSSLVELVGDPVGARQRLMCRLPKRPDPHAWLGDAFHAWVQQFYGAELLFDLGDLPGAADREVGDPEELAALQRAFTASSWAARTPAAVEVPFEMP
IGDTVVRGRIDAVFVDPDGGATVVDWKTGKPPHGPAAMRQAAVQLAVYRLAWAALRGCPTSSVRTAFYYVRSGITVVPDELPAPGELAMLLTDCAGRRSD
T

(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

Rv3201c/-, gene len: 3305 bp, num TA sites: 48

condition	dataset	call	medium	method	notes
in-vitro	DeJesus 2017 mBio	non-essential	7H9	HMM	fully saturated, 14 TnSeq libraries combined
in-vitro	Sassetti 2003 Mol Micro	essential	7H9	TRASH	essential if hybridization ratio<0.2
in-vivo (mice)	Sassetti 2003 PNAS	non-essential	BL6 mice	TRASH	essential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)
in-vitro (glycerol)	Griffin 2011 PPath	uncertain	M9 minimal+glycerol	Gumbel	2 replicates; Padj<0.05
in-vitro (cholesterol)	Griffin 2011 PPath	uncertain	M9 minimal+cholesterol	Gumbel	3 replicates; Padj<0.05
differentially essential in cholesterol	Griffin 2011 PPath	NO (LFC=-0.19)	cholesterol vs glycerol	resampling-SR	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol
in-vitro	Smith 2022 eLife	non-essential	7H9	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice)	Smith 2022 eLife	non-essential	BL6 mice	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice	Smith 2022 eLife	NO (LFC=0.487)	in-vivo vs in-vitro	ZINB	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice
in-vitro (minimal)	Minato 2019 mSys	non-essential	minimal medium	HMM
in-vitro (YM rich medium)	Minato 2019 mSys	non-essential	YM rich medium	HMM	7H9 supplemented with ~20 metabolites (amino acids, cofactors)
differentially essential in YM rich medium	Minato 2019 mSys	NO (LFC=-0.23)	YM rich vs minimal medium	resampling

Analysis of Positive Selection in Clinical Isolates new

data from Culviner et al (2025) (55,259 Mtb clinical isolates)
- overall pN/pS for Rv3201c: 0.582071352
- lineage-specific pN/pS in L1: 0.543952357
- lineage-specific pN/pS in L2: 0.56087808
- lineage-specific pN/pS in L3: 0.737639656
- lineage-specific pN/pS in L4: 0.56468521

Analysis of dN/dS (omega) in a global collection of 10k Mtb clinical isolates using GenomegaMap (Window model)
clinical isolates collection: global set of 10,626 Mtb genomes
In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	global set of 10,626 Mtb clinical isolates
under significant positive selection?	NO
omega peak height (95%CI lower bound)	1.22 (0.61)
codons under selection
omega plots
genetic variants*	link

* example format for variants: "D27 (GAC): D27H (CAC,11)" means "Asp27 (native codon GAC) mutated to His (codon CAC) in 11 isolates"

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: see table of TFOE interactions below

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:
- No bindings to other targets were found.

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

TFOE = Transcription Factor Over-Expression study
significance criteria used in paper: greater than 2-fold change (|LFC|>=1.0) and Padj<0.01

gene	dysregulated by OE of	LFC
Rv3201c/-	Rv1219c/-	2.09
Rv3201c/-	Rv2884/-	2.06
Rv3201c/-	Rv0818/glnR	1.76
Rv3201c/-	Rv0576/-	1.3
Rv3201c/-	Rv1990c/-	1.21
Rv3201c/-	Rv2827c/-	1.15
Rv3201c/-	Rv0081/-	1.07
Rv3201c/-	Rv3574/kstR	1.04
Rv3201c/-	Rv3849/espR	-1.11
Rv3201c/-	Rv0182c/sigG	-1.17
Rv3201c/-	Rv0023/-	-1.21
Rv3201c/-	Rv0078/-	-1.23
Rv3201c/-	Rv3223c/sigH	-1.23
Rv3201c/-	Rv0022c/whiB5	-1.47

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

Property	Value	Creator	Evidence	PMID	Comment
Other	TBPWY:NER and related	vmizrahi			Expressed following DNA damage
Other	TBPWY:NER and related	vmizrahi			Shows elevated expresson in clinical lung samples

TB Genome Annotation Portal