Rv2163c (pbpB)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: cell division protein FtsI (penicillin-binding protein 3)
- REFSEQ: penicillin-binding membrane protein pbpB
- PATRIC: Cell division protein FtsI [Peptidoglycan synthetase] (EC 2.4.1.129)
- TUBERCULIST: Probable penicillin-binding membrane protein PbpB
- NCBI: Probable penicillin-binding membrane protein PbpB
- updated information (H37Rv4):
  - gene name: pbpB
  - function: aka FtsI or pbp3
  - reference: Datta (2006) PMID: 17427288
Type: Not Target
Start: 2425048
End: 2427087
Operon:

Trans-membrane region:
Role: II.C.3 - Murein sacculus and peptidoglycan
GO terms:
- GO:0071555 - cell wall organization (Uniprot)
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0009252 - peptidoglycan biosynthetic process (Uniprot)
- GO:0008658 - penicillin binding (Uniprot)
- GO:0008360 - regulation of cell shape (Uniprot)
- GO:0005886 - plasma membrane (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
6KGW	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Penicillin binding protein 3 (PBP3) from Mycobacterium tuerculosis, complexed with ampicillin
6KGV	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Penicillin binding protein 3 (PBP3) from Mycobacterium tuerculosis, complexed with amoxicillin
6KGU	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Penicillin binding protein 3 (PBP3) from Mycobacterium tuerculosis, complexed with aztreonam
6KGT	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Penicillin binding protein 3 (PBP3) from Mycobacterium tuerculosis, complexed with faropenem
6KGS	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Penicillin binding protein 3 (PBP3) from Mycobacterium tuerculosis, complexed with meropenem
6KGH	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Penicillin binding protein 3 (PBP3) from Mycobacterium tuerculosis (apo-form)

Links to additional information on pbpB:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -5.089 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VSRAAPRRASQSQSTRPARGLRRPPGAQEVGQRKRPGKTQKARQAQEATKSRPATRSDVAPAGRSTRARRTRQVVDVGTRGASFVFRHRTGNAVILVLML
VAATQLFFLQVSHAAGLRAQAAGQLKVTDVQPAARGSIVDRNNDRLAFTIEARALTFQPKRIRRQLEEARKKTSAAPDPQQRLRDIAQEVAGKLNNKPDA
AAVLKKLQSDETFVYLARAVDPAVASAICAKYPEVGAERQDLRQYPGGSLAANVVGGIDWDGHGLLGLEDSLDAVLAGTDGSVTYDRGSDGVVIPGSYRN
RHKAVHGSTVVLTLDNDIQFYVQQQVQQAKNLSGAHNVSAVVLDAKTGEVLAMANDNTFDPSQDIGRQGDKQLGNPAVSSPFEPGSVNKIVAASAVIEHG
LSSPDEVLQVPGSIQMGGVTVHDAWEHGVMPYTTTGVFGKSSNVGTLMLSQRVGPERYYDMLRKFGLGQRTGVGLPGESAGLVPPIDQWSGSTFANLPIG
QGLSMTLLQMTGMYQAIANDGVRVPPRIIKATVAPDGSRTEEPRPDDIRVVSAQTAQTVRQMLRAVVQRDPMGYQQGTGPTAGVPGYQMAGKTGTAQQIN
PGCGCYFDDVYWITFAGIATADNPRYVIGIMLDNPARNSDGAPGHSAAPLFHNIAGWLMQRENVPLSPDPGPPLVLQAT

(Nucleotide sequence available on KEGG)

Additional Information

pbpB, also known as ftsI or pbp3

Datta et al (2006)  https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2958.2006.05491.x

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; 29 non-insertions in a row out of 29 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 29 non-insertions in a row out of 29 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 29 non-insertions in a row out of 29 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 29 non-insertions in a row out of 30 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 29 non-insertions in a row out of 30 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.03
Essential-Domain	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)
- Rv1816 (-) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0880 (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:

Property	Value	Creator	Evidence	PMID	Comment
Name	Class B penicillin binding protein	mjackson	IMP		Cell division
Name	Class B penicillin binding protein	mjackson	IDA		Cell division
Symbol	FtsI	rslayden			RA. Slayden & JT. Belisle Morphological features and signature gene response elicited by inactivation of FtsI in Mycobacterium tuberculosis. J. Antimicrob. Chemother. 2008
Name	Cell division protein, PG complex	rslayden			RA. Slayden & JT. Belisle Morphological features and signature gene response elicited by inactivation of FtsI in Mycobacterium tuberculosis. J. Antimicrob. Chemother. 2008
Citation	Morphological features and signature gene response elicited by inactivation of FtsI in Mycobacterium tuberculosis. RA. Slayden & JT. Belisle J. Antimicrob. Chemother. 2008	rslayden		19109339	None

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