Rv3343c (PPE54)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: PPE family protein
- REFSEQ: PPE family protein
- PATRIC: PPE family protein
- TUBERCULIST: PPE family protein PPE54
- NCBI: PPE family protein PPE54
- updated information (H37Rv4):
  - gene name: PPE54
  - function:
  - reference:
Type: Essential
Start: 3729364
End: 3736935
Operon:

Trans-membrane region:
Role: IV.C.2 - PPE family
GO terms:
- GO:0052170 - negative regulation by symbiont of host innate immune response (Uniprot)
- GO:0040007 - growth (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
5XFS	52%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of PE8-PPE15 in complex with EspG5 from M. tuberculosis
6VHR	41%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Structure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) secretion system, space group I422
6UUJ	41%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Structure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) secretion system, space group P212121

Links to additional information on PPE54:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.995 (from Jeremy Rock's lab)
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology
- KEGG - nucleotide and amino acid sequences of gene

Amino Acid Sequence

MSFVVMPPEINSLLIYTGAGPGPLLAAAAAWDELAAELGSAAAAFGSVTSGLVGGIWQGPSSVAMAAAAAPYAGWLSAAAASAESAAGQARAVVGVFEAA
LAETVDPFVIAANRSRLVSLALSNLFGQNTPAIAAAEFDYELMWAQDVAAMLGYHTGASAAAEALAPFGSPLASLAAAAEPAKSLAVNLGLANVGLFNAG
SGNVGSYNVGAGNVGSYNVGGGNIGGNNVGLGNVGWGNFGLGNSGLTPGLMGLGNIGFGNAGSYNFGLANMGVGNIGFANTGSGNFGIGLTGDNLTGFGG
FNTGSGNVGLFNSGTGNVGFFNSGTGNWGVFNSGSYNTGIGNSGIASTGLFNAGGFNTGVVNAGSYNTGSFNAGEANTGGFNPGSVNTGWLNTGDINTGV
ANSGDVNTGAFISGNYSNGVLWRGDYQGLLGFSSGANVLPVIPLSLDINGGVGAITIEPIHILPDIPININETLYLGPLVVPPINVPAISLGVGIPNISI
GPIKINPITLWPAQNFNQTITLAWPVSSITIPQIQQVALSPSPIPTTLIGPIHINTGFSIPVTFSYSTPALTLFPVGLSIPTGGPLTLTLGVTAGTEAFT
IPGFSIPEQPLPLAINVIGHINALSTPAITIDNIPLNLHAIGGVGPVDIVGGNVPASPGFGNSTTAPSSGFFNTGAGGVSGFGNVGAHTSGWFNQSTQAM
QVLPGTVSGYFNSGTLMSGIGNVGTQLSGMLSGGALGGNNFGLGNIGFDNVGFGNAGSSNFGLANMGIGNIGLANTGNGNIGIGLSGDNLTGFGGFNSGS
ENVGLFNSGTGNVGFFNSGTGNLGVFNSGSHNTGFFLTGNNINVLAPFTPGTLFTISEIPIDLQVIGGIGPIHVQPIDIPAFDIQITGGFIGIREFTLPE
ITIPAIPIHVTGTVGLEGFHVNPAFVLFGQTAMAEITADPVVLPDPFITIDHYGPPLGPPGAKFPSGSFYLSISDLQINGPIIGSYGGPGTIPGPFGATF
NLSTSSLALFPAGLTVPDQTPVTVNLTGGLDSITLFPGGLAFPENPVVSLTNFSVGTGGFTVFPQGFTVDRIPVDLHTTLSIGPFPFRWDYIPPTPANGP
IPAVPGGFGLTSGLFPFHFTLNGGIGPISIPTTTVVDALNPLLTVTGNLEVGPFTVPDIPIPAINFGLDGNVNVSFNAPATTLLSGLGITGSIDISGIQI
TNIQTQPAQLFMSVGQTLFLFDFRDGIELNPIVIPGSSIPITMAGLSIPLPTVSESIPLNFSFGSPASTVKSMILHEILPIDVSINLEDAVFIPATVLPA
IPLNVDVTIPVGPINIPIITEPGSGNSTTTTSDPFSGLAVPGLGVGLLGLFDGSIANNLISGFNSAVGIVGPNVGLSNLGGGNVGLGNVGDFNLGAGNVG
GFNVGGGNIGGNNVGLGNVGFGNVGLANSGLTPGLMGLGNIGFGNAGSYNFGLANMGVGNIGFANTGSGNFGIGLTGDNLTGFGGFNTGSGNVGLFNSGT
GNVGFFNSGTGNWGVFNSGSYNTGIGNSGIASTGLFNAGGFNTGVVNAGSYNTGSFNAGQANTGGFNPGSVNTGWLNTGDINTGVANSGDVNTGAFISGN
YSNGAFWRGDYQGLLGFSYRPAVLPQTPFLDLTLTGGLGSVVIPAIDIPAIRPEFSANVAIDSFTVPSIPIPQIDLAATTVSVGLGPITVPHLDIPRVPV
TLNYLFGSQPGGPLKIGPITGLFNTPIGLTPLALSQIVIGASSSQGTITAFLANLPFSTPVVTIDEIPLLASITGHSEPVDIFPGGLTIPAMNPLSINLS
GGTGAVTIPAITIGEIPFDLVAHSTLGPVHILIDLPAVPGFGNTTGAPSSGFFNSGAGGVSGFGNVGAMVSGGWNQAPSALLGGGSGVFNAGTLHSGVLN
FGSGMSGLFNTSVLGLGAPALVSGLGSVGQQLSGLLASGTALHQGLVLNFGLADVGLGNVGLGNVGDFNLGAGNVGGFNVGGGNIGGNNVGLGNVGWGNF
GLGNSGLTPGLMGLGNIGFGNAGSYNFGLANMGVGNIGFANTGSGNFGIGLTGDNLTGFGGFNTGSGNVGLFNSGTGNVGFFNSGTGNWGVFNSGSYNTG
IGNSGIASTGLFNAGGFNTGVVNAGSYNTGSFNAGQANTGGFNPGSVNTGWLNTGDINTGVANSGDVNTGAFISGNYSNGAFWRGDYQGLLGFSYTSTII
PEFTVANIHASGGAGPIIVPSIQFPAIPLDLSATGHIGGFTIPPVSISPITVRIDPVFDLGPITVQDITIPALGLDPATGVTVGPIFSSGSIIDPFSLTL
LGFINVNVPAIQTAPSEILPFTVLLSSLGVTHLTPEITIPGFHIPVDPIHVELPLSVTIGPFVSPEITIPQLPLGLALSGATPAFAFPLEITIDRIPVVL
DVNALLGPINAGLVIPPVPGFGNTTAVPSSGFFNIGGGGGLSGFHNLGAGMSGVLNAISDPLLGSASGFANFGTQLSGILNRGADISGVYNTGALGLITS
ALVSGFGNVGQQLAGLIYTGTGP

(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; 9 non-insertions in a row out of 156 sites
Uncertain	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.758800; 14 non-insertions in a row out of 156 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 9 non-insertions in a row out of 156 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.999900; 18 non-insertions in a row out of 131 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 23 non-insertions in a row out of 131 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.1
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:
- Rv0047c (-) (Direct binding)
- Rv1423 (whiA) (Direct binding)
- Rv3849 (espR) (Direct binding)

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:
- Rv0023 (-)
- Rv3417c (groEL1)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	PhysicalInteraction Rv3344c	vashishtrv	RCA		Gene neighbourhood (Functional linkage) authors,NC. Gey van Pittius,SL. Sampson,H. Lee,Y. Kim,PD. van Helden,RM. Warren Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC Evol. Biol. 2006
Interaction	PhysicalInteraction Rv3344c	vashishtrv	RCA		Gene neighbourhood (Functional linkage) AJ. Vallecillo & C. Espitia Expression of Mycobacterium tuberculosis pe_pgrs33 is repressed during stationary phase and stress conditions, and its transcription is mediated by sigma factor A. Microb. Pathog. 2008
Interaction	PhysicalInteraction Rv3344c	vashishtrv	RCA		Gene neighbourhood (Functional linkage) authors,NC. Gey van Pittius,SL. Sampson,H. Lee,Y. Kim,PD. van Helden,RM. Warren Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC Evol. Biol. 2006
Citation	Regulation of the Mycobacterium tuberculosis PE/PPE genes. MI. Voskuil,D. Schnappinger,R. Rutherford,Y. Liu,GK. Schoolnik Tuberculosis (Edinb) 2004	vashishtrv	RCA	15207495	Gene neighbourhood (Functional linkage)
Interaction	PhysicalInteraction Rv3344c	vashishtrv	RCA		Gene neighbourhood (Functional linkage) MI. Voskuil,D. Schnappinger,R. Rutherford,Y. Liu,GK. Schoolnik Regulation of the Mycobacterium tuberculosis PE/PPE genes. Tuberculosis (Edinb) 2004
Interaction	PhysicalInteraction Rv3344c	shahanup86	RCA		Gene neighbourhood (Functional linkage) authors,NC. Gey van Pittius,SL. Sampson,H. Lee,Y. Kim,PD. van Helden,RM. Warren Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC Evol. Biol. 2006
Interaction	PhysicalInteraction Rv3344c	shahanup86	RCA		Gene neighbourhood (Functional linkage) AJ. Vallecillo & C. Espitia Expression of Mycobacterium tuberculosis pe_pgrs33 is repressed during stationary phase and stress conditions, and its transcription is mediated by sigma factor A. Microb. Pathog. 2008
Citation	Characterization of a Mycobacterium tuberculosis H37Rv transposon library reveals insertions in 351 ORFs and mutants with altered virulence. RA. McAdam, S. Quan et al. Microbiology (Reading, Engl.) 2002	shahanup86	RCA	12368431	Gene neighbourhood (Functional linkage)
Interaction	PhysicalInteraction Rv3344c	shahanup86	RCA		Gene neighbourhood (Functional linkage) RA. McAdam, S. Quan et al. Characterization of a Mycobacterium tuberculosis H37Rv transposon library reveals insertions in 351 ORFs and mutants with altered virulence. Microbiology (Reading, Engl.) 2002
Citation	Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. authors,NC. Gey van Pittius,SL. Sampson,H. Lee,Y. Kim,PD. van Helden,RM. Warren BMC Evol. Biol. 2006	shahanup86	RCA	17105670	Gene neighbourhood (Functional linkage)
Interaction	PhysicalInteraction Rv3344c	shahanup86	RCA		Gene neighbourhood (Functional linkage) authors,NC. Gey van Pittius,SL. Sampson,H. Lee,Y. Kim,PD. van Helden,RM. Warren Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC Evol. Biol. 2006
Citation	Regulation of the Mycobacterium tuberculosis PE/PPE genes. MI. Voskuil,D. Schnappinger,R. Rutherford,Y. Liu,GK. Schoolnik Tuberculosis (Edinb) 2004	shahanup86	RCA	15207495	Gene neighbourhood (Functional linkage)
Interaction	PhysicalInteraction Rv3344c	shahanup86	RCA		Gene neighbourhood (Functional linkage) MI. Voskuil,D. Schnappinger,R. Rutherford,Y. Liu,GK. Schoolnik Regulation of the Mycobacterium tuberculosis PE/PPE genes. Tuberculosis (Edinb) 2004
Citation	Characterization of a Mycobacterium tuberculosis H37Rv transposon library reveals insertions in 351 ORFs and mutants with altered virulence. RA. McAdam, S. Quan et al. Microbiology (Reading, Engl.) 2002	vashishtrv	RCA	12368431	Gene neighbourhood (Functional linkage)
Interaction	PhysicalInteraction Rv3344c	vashishtrv	RCA		Gene neighbourhood (Functional linkage) RA. McAdam, S. Quan et al. Characterization of a Mycobacterium tuberculosis H37Rv transposon library reveals insertions in 351 ORFs and mutants with altered virulence. Microbiology (Reading, Engl.) 2002
Citation	Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. authors,NC. Gey van Pittius,SL. Sampson,H. Lee,Y. Kim,PD. van Helden,RM. Warren BMC Evol. Biol. 2006	vashishtrv	RCA	17105670	Gene neighbourhood (Functional linkage)

TB Genome Annotation Portal