Rv3800c (pks13)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: polyketide synthase 13
- REFSEQ: polyketide synthase PKS13
- PATRIC: Probable polyketide synthase similar to many. e.g. gp|M63676|SERERYAA_1 S.erythraea first ORF of eryA gene involved in complex polyketide formation in erythromycin biosynthesis.
- TUBERCULIST: Polyketide synthase Pks13
- NCBI: Polyketide synthase Pks13
- updated information (H37Rv4):
  - gene name: pks13
  - function:
  - reference:
Type: Not Target
Start: 4255945
End: 4261146
Operon:

Trans-membrane region:
Role: I.I - Polyketide and non-ribosomal peptide synthesis
GO terms:
- GO:0031177 - phosphopantetheine binding (Uniprot)
- GO:0016788 - hydrolase activity, acting on ester bonds (Uniprot)
- GO:0009058 - biosynthetic process (Uniprot)
- GO:0008152 - metabolic process (Uniprot)
- GO:0003824 - catalytic activity (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- HEXACOSANOYL_COA_CO2[c] + MEROACYL_AMP[c] -> CO2[c] + COA[c] + AMP[c] + C78_3_OXY_MYCOLATE_ENZ[c]
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: 3tzw, 3tzx, 3tzy, 3tzz
Search for Homologs in PDB

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

PDB	aa ident	species	PDB title
6D8J	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis polyketide synthase 13 N-terminal acyl carrier protein domain
6D8I	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis polyketide synthase 13 N-terminal acyl carrier protein domain
6C4Q	100%	Mycobacterium tuberculosis	1.16 Angstrom Resolution Crystal Structure of Acyl Carrier Protein Domain (residues 1-100) of Polyketide Synthase Pks13 from Mycobacterium tuberculosis
5XUO	100%	Mycobacterium tuberculosis H37Rv	Pks13 AT domain fragment from Mycobacterium tuberculosis
5V42	100%	Mycobacterium tuberculosis	Crystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor TAM3
5V41	100%	Mycobacterium tuberculosis	Crystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor TAM5
5V40	100%	Mycobacterium tuberculosis	Crystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor TAM6
5V3Y	100%	Mycobacterium tuberculosis	Crystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor TAM16
5V3X	100%	Mycobacterium tuberculosis	Crystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor TAM1
5V3W	100%	Mycobacterium tuberculosis	Crystal Structure of the Apo form of Thioesterase domain of Mtb Pks13

Links to additional information on pks13:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -9.055 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology
- Photo of spot titer

Amino Acid Sequence

MADVAESQENAPAERAELTVPEMRQWLRNWVGKAVGKAPDSIDESVPMVELGLSSRDAVAMAADIEDLTGVTLSVAVAFAHPTIESLATRIIEGEPETDL
AGDDAEDWSRTGPAERVDIAIVGLSTRFPGEMNTPEQTWQALLEGRDGITDLPDGRWSEFLEEPRLAARVAGARTRGGYLKDIKGFDSEFFAVAKTEADN
IDPQQRMALELTWEALEHARIPASSLRGQAVGVYIGSSTNDYSFLAVSDPTVAHPYAITGTSSSIIANRVSYFYDFHGPSVTIDTACSSSLVAIHQGVQA
LRNGEADVVVAGGVNALITPMVTLGFDEIGAVLAPDGRIKSFSADADGYTRSEGGGMLVLKRVDDARRDGDAILAVIAGSAVNHDGRSNGLIAPNQDAQA
DVLRRAYKDAGIDPRTVDYIEAHGTGTILGDPIEAEALGRVVGRGRPADRPALLGAVKTNVGHLESAAGAASMAKVVLALQHDKLPPSINFAGPSPYIDF
DAMRLKMITTPTDWPRYGGYALAGVSSFGFGGANAHVVVREVLPRDVVEKEPEPEPEPKAAAEPAEAPTLAGHALRFDEFGNIITDSAVAEEPEPELPGV
TEEALRLKEAALEELAAQEVTAPLVPLAVSAFLTSRKKAAAAELADWMQSPEGQASSLESIGRSLSRRNHGRSRAVVLAHDHDEAIKGLRAVAAGKQAPN
VFSVDGPVTTGPVWVLAGFGAQHRKMGKSLYLRNEVFAAWIEKVDALVQDELGYSVLELILDDAQDYGIETTQVTIFAIQIALGELLRHHGAKPAAVIGQ
SLGEAASAYFAGGLSLRDATRAICSRSHLMGEGEAMLFGEYIRLMALVEYSADEIREVFSDFPDLEVCVYAAPTQTVIGGPPEQVDAILARAEAEGKFAR
KFATKGASHTSQMDPLLGELTAELQGIKPTSPTCGIFSTVHEGRYIKPGGEPIHDVEYWKKGLRHSVYFTHGIRNAVDSGHTTFLELAPNPVALMQVALT
TADAGLHDAQLIPTLARKQDEVSSMVSTMAQLYVYGHDLDIRTLFSRASGPQDYANIPPTRFKRKEHWLPAHFSGDGSTYMPGTHVALPDGRHVWEYAPR
DGNVDLAALVRAAAAHVLPDAQLTAAEQRAVPGDGARLVTTMTRHPGGASVQVHARIDESFTLVYDALVSRAGSESVLPTAVGAATAIAVADGAPVAPET
PAEDADAETLSDSLTTRYMPSGMTRWSPDSGETIAERLGLIVGSAMGYEPEDLPWEVPLIELGLDSLMAVRIKNRVEYDFDLPPIQLTAVRDANLYNVEK
LIEYAVEHRDEVQQLHEHQKTQTAEEIARAQAELLHGKVGKTEPVDSEAGVALPSPQNGEQPNPTGPALNVDVPPRDAAERVTFATWAIVTGKSPGGIFN
ELPRLDDEAAAKIAQRLSERAEGPITAEDVLTSSNIEALADKVRTYLEAGQIDGFVRTLRARPEAGGKVPVFVFHPAGGSTVVYEPLLGRLPADTPMYGF
ERVEGSIEERAQQYVPKLIEMQGDGPYVLVGWSLGGVLAYACAIGLRRLGKDVRFVGLIDAVRAGEEIPQTKEEIRKRWDRYAAFAEKTFNVTIPAIPYE
QLEELDDEGQVRFVLDAVSQSGVQIPAGIIEHQRTSYLDNRAIDTAQIQPYDGHVTLYMADRYHDDAIMFEPRYAVRQPDGGWGEYVSDLEVVPIGGEHI
QAIDEPIIAKVGEHMSRALGQIEADRTSEVGKQ

(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
Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 58 non-insertions in a row out of 58 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 58 non-insertions in a row out of 58 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 58 non-insertions in a row out of 58 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 58 non-insertions in a row out of 58 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 58 non-insertions in a row out of 58 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.05
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:
- Rv0023 (-)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv2009 (vapB15) (Direct binding)
- Rv0678 (-) (Upstream of operon)
- Rv1033c (trcR) (Upstream of operon)

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 (-)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	PhysicalInteraction Rv3801c	sourish10	TAS		Affinity purification (Physical interaction) SK. Parker, RM. Barkley et al. Mycobacterium tuberculosis Rv3802c encodes a phospholipase/thioesterase and is inhibited by the antimycobacterial agent tetrahydrolipstatin. PLoS ONE 2009
Interaction	ActivatedBy Rv2794c	shahanup86	IDA		Affinity purification (Physical interaction) C. Chalut, L. Botella et al. The nonredundant roles of two 4'-phosphopantetheinyl transferases in vital processes of Mycobacteria. Proc. Natl. Acad. Sci. U.S.A. 2006
Name	polyketide synthase 13	mjackson	IMP		Claisen-type condensation
Name	polyketide synthase 13	mjackson	IDA		Claisen-type condensation
Citation	Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis. K. Takayama, C. Wang et al. Clin. Microbiol. Rev. 2005	jjmcfadden		15653820	Inferred from direct assay
Other	EC:	jjmcfadden			Inferred from direct assay K. Takayama, C. Wang et al. Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis. Clin. Microbiol. Rev. 2005
Citation	Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria. OA. Trivedi,P. Arora,V. Sridharan,R. Tickoo,D. Mohanty,RS. Gokhale Nature 2004	extern:JZUCKER		15042094	Inferred from experiment
Term	EC:2.1.1.- Transferases. Transferring one-carbon groups. Methyltransferases. - NR	extern:JZUCKER	NR		Inferred from experiment OA. Trivedi,P. Arora,V. Sridharan,R. Tickoo,D. Mohanty,RS. Gokhale Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria. Nature 2004
Citation	Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis. K. Takayama, C. Wang et al. Clin. Microbiol. Rev. 2005	extern:JZUCKER		15653820	Traceable author statement
Term	EC:2.1.1.- Transferases. Transferring one-carbon groups. Methyltransferases. - NR	extern:JZUCKER	NR		Traceable author statement K. Takayama, C. Wang et al. Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis. Clin. Microbiol. Rev. 2005

TB Genome Annotation Portal