Rv3666c (dppA)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: peptide/nickel transporter substrate-binding protein
- REFSEQ: periplasmic dipeptide-binding lipoprotein DppA
- PATRIC: Dipeptide-binding ABC transporter periplasmic substrate-binding component (TC 3.A.1.5.2)
- TUBERCULIST: Probable periplasmic dipeptide-binding lipoprotein DppA
- NCBI: Probable periplasmic dipeptide-binding lipoprotein DppA
- updated information (H37Rv4):
  - gene name: dppA
  - function: implicated in heme uptake
  - reference: Mitra 2017; PMID: 28119467
Type: Not Target
Start: 4105459
End: 4107084
Operon:

Trans-membrane region:
Role: III.A.1 - Amino acids
GO terms:
- GO:0055085 - transmembrane transport (Uniprot)
- GO:0043190 - ATP-binding cassette (ABC) transporter complex (Uniprot)
- GO:0030288 - outer membrane-bounded periplasmic space (Uniprot)
- GO:0015833 - peptide transport (Uniprot)
- GO:0015197 - not-found (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

6E4D 99% Mycobacterium tuberculosis Atomic structure of Mycobacterium tuberculosis DppA

6E3D 99% Mycobacterium tuberculosis Atomic structure of Mycobacterium tuberculosis DppA
Links to additional information on dppA:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.158 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

PDB	aa ident	species	PDB title
6E4D	99%	Mycobacterium tuberculosis	Atomic structure of Mycobacterium tuberculosis DppA
6E3D	99%	Mycobacterium tuberculosis	Atomic structure of Mycobacterium tuberculosis DppA

Amino Acid Sequence

MVRQMRAALAALATGLLVLAPVAGCGGGVLSPDVVLVNGGEPPNPLIPTGTNDSNGGRIIDRLFAGLMSYDAVGKPSLEVAQSIESADNVNYRITVKPGW
KFTDGSPVTAHSFVDAWNYGALSTNAQLQQHFFSPIEGFDDVAGAPGDKSRTTMSGLRVVNDLEFTVRLKAPTIDFTLRLGHSSFYPLPDSAFRDMAAFG
RNPIGNGPYKLADGPAGPAWEHNVRIDLVPNPDYHGNRKPRNKGLRFEFYANLDTAYADLLSGNLDVLDTIPPSALTVYQRDLGDHATSGPAAINQTLDT
PLRLPHFGGEEGRLRRLALSAAINRPQICQQIFAGTRSPARDFTARSLPGFDPNLPGNEVLDYDPQRARRLWAQADAISPWSGRYAIAYNADAGHRDWVD
AVANSIKNVLGIDAVAAPQPTFAGFRTQITNRAIDSAFRAGWRGDYPSMIEFLAPLFTAGAGSNDVGYINPEFDAALAAAEAAPTLTESHELVNDAQRIL
FHDMPVVPLWDYISVVGWSSQVSNVTVTWNGLPDYENIVKA

(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
Uncertain	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.908300; 10 non-insertions in a row out of 23 sites
Uncertain	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.694450; 7 non-insertions in a row out of 23 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.004800; 6 non-insertions in a row out of 23 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.062350; 7 non-insertions in a row out of 23 sites
Uncertain	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.976300; 9 non-insertions in a row out of 23 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.2
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:
- No bindings to other targets were found.

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv3416 (whiB3)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0576 (-)
- Rv2887 (-)

TB Genome Annotation Portal