Rv0050 (ponA1)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: peptidoglycan glycosyltransferase
- REFSEQ: bifunctional penicillin-binding protein 1A/1B
- PATRIC: Multimodular transpeptidase-transglycosylase (EC 2.4.1.129) (EC 3.4.-.-)
- TUBERCULIST: Probable bifunctional penicillin-binding protein 1A/1B PonA1 (murein polymerase) (PBP1): penicillin-insensitive transglycosylase (peptidoglycan TGASE) + penicillin-sensitive transpeptidase (DD-transpeptidase)
- NCBI: Probable bifunctional penicillin-binding protein 1A/1B PonA1 (murein polymerase) (PBP1): penicillin-insensitive transglycosylase (peptidoglycan TGASE) + penicillin-sensitive transpeptidase (DD-transpeptidase)
- updated information (H37Rv4):
  - gene name: ponA1
  - function:
  - reference:
Type: Not Target
Start: 53663
End: 55699
Operon:

Trans-membrane region:
Role: II.C.3 - Murein sacculus and peptidoglycan
GO terms:
- GO:0071555 - cell wall organization (Uniprot)
- GO:0071456 - cellular response to hypoxia (Uniprot)
- GO:0030288 - outer membrane-bounded periplasmic space (Uniprot)
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0016757 - transferase activity, transferring glycosyl groups (Uniprot)
- GO:0016740 - transferase activity (Uniprot)
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0009252 - peptidoglycan biosynthetic process (Uniprot)
- GO:0009002 - serine-type D-Ala-D-Ala carboxypeptidase activity (Uniprot)
- GO:0008955 - peptidoglycan glycosyltransferase activity (Uniprot)
- GO:0008658 - penicillin binding (Uniprot)
- GO:0008360 - regulation of cell shape (Uniprot)
- GO:0008233 - peptidase activity (Uniprot)
- GO:0008152 - metabolic process (Uniprot)
- GO:0006508 - proteolysis (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0004180 - carboxypeptidase activity (Uniprot)
- GO:0003824 - catalytic activity (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
5CXW	100%	Mycobacterium tuberculosis	Structure of the PonA1 protein from Mycobacterium Tuberculosis in complex with penicillin V
5CRF	100%	Mycobacterium tuberculosis	Structure of the penicillin-binding protein PonA1 from Mycobacterium Tuberculosis
3NB7	40%	Aquifex aeolicus	Crystal structure of Aquifex Aeolicus Peptidoglycan Glycosyltransferase in complex with Decarboxylated Neryl Moenomycin
3NB6	40%	Aquifex aeolicus	Crystal structure of Aquifex aeolicus peptidoglycan glycosyltransferase in complex with Methylphosphoryl Neryl Moenomycin
3D3H	40%	Aquifex aeolicus	Crystal structure of a complex of the peptidoglycan glycosyltransferase domain from Aquifex aeolicus and neryl moenomycin A
2OQO	40%	Aquifex aeolicus	Crystal structure of a peptidoglycan glycosyltransferase from a class A PBP: insight into bacterial cell wall synthesis
5ZZK	35%	Staphylococcus aureus	A Con Artist: Phenylphenoxybenzamide is not a Glycosyltransferase Inhibitor
3VMT	35%	Staphylococcus aureus	Crystal structure of Staphylococcus aureus membrane-bound transglycosylase in complex with a Lipid II analog
3VMS	35%	Staphylococcus aureus	Crystal structure of Staphylococcus aureus membrane-bound transglycosylase in complex with NBD-Lipid II
3VMR	35%	Staphylococcus aureus	Crystal structure of Staphylococcus aureus membrane-bound transglycosylase in complex with moenomycin

Links to additional information on ponA1:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -1.052 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VVILLPMVTFTMAYLIVDVPKPGDIRTNQVSTILASDGSEIAKIVPPEGNRVDVNLSQVPMHVRQAVIAAEDRNFYSNPGFSFTGFARAVKNNLFGGDLQ
GGSTITQQYVKNALVGSAQHGWSGLMRKAKELVIATKMSGEWSKDDVLQAYLNIIYFGRGAYGISAASKAYFDKPVEQLTVAEGALLAALIRRPSTLDPA
VDPEGAHARWNWVLDGMVETKALSPNDRAAQVFPETVPPDLARAENQTKGPNGLIERQVTRELLELFNIDEQTLNTQGLVVTTTIDPQAQRAAEKAVAKY
LDGQDPDMRAAVVSIDPHNGAVRAYYGGDNANGFDFAQAGLQTGSSFKVFALVAALEQGIGLGYQVDSSPLTVDGIKITNVEGEGCGTCNIAEALKMSLN
TSYYRLMLKLNGGPQAVADAAHQAGIASSFPGVAHTLSEDGKGGPPNNGIVLGQYQTRVIDMASAYATLAASGIYHPPHFVQKVVSANGQVLFDASTADN
TGDQRIPKAVADNVTAAMEPIAGYSRGHNLAGGRDSAAKTGTTQFGDTTANKDAWMVGYTPSLSTAVWVGTVKGDEPLVTASGAAIYGSGLPSDIWKATM
DGALKGTSNETFPKPTEVGGYAGVPPPPPPPEVPPSETVIQPTVEIAPGITIPIGPPTTITLAPPPPAPPAATPTPPP

(Nucleotide sequence available on KEGG)

Additional Information

Analysis of Positive Selection in Clinical Isolates new

Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
- Moldova: 2,057 clinical isolates
- global set: 5,195 clinical isolates from 15 other countries
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.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	1.27 (0.36)	1.39 (0.72)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link

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

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across ~100 conditions

Rv0050/ponA1, gene len: 2036 bp, num TA sites: 37

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	non-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	non-essential	M9 minimal+glycerol	Gumbel	2 replicates; Padj<0.05
in-vitro (cholesterol)	Griffin 2011 PPath	non-essential	M9 minimal+cholesterol	Gumbel	3 replicates; Padj<0.05
differentially essential in cholesterol	Griffin 2011 PPath	NO (LFC=0.65)	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=-0.002)	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	essential	YM rich medium	HMM	7H9 supplemented with ~20 metabolites (amino acids, vitamins)
differentially essential in YM rich medium	Minato 2019 mSys	YES (LFC=-3.88)	YM rich vs minimal medium	resampling

TnSeq Data

collected by Karen Kieser (Rubin lab, ca. 2015)
insertion counts: dPonA1_KOD.wig
reference data: glycerol_H37Rv_merged.wig
resampling results: resampling_H37Rv_glycerol_ponA1KO_s10000_pc0.00.xlsx (significant conditionally essential genes are those with Padj<0.05)
SRA: SRA277968
PATRIC: https://docs.patricbrc.org/news/2016/20160121-flute-experiment-2.html
publication: Kieser et al (2015). Peptidoglycan synthesis in Mycobacterium tuberculosis is organized into networks with varying drug susceptibility. PNAS, 112(42):13087-13092.

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:
- No bindings from other targets were found.

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0967 (csoR) (Direct binding)
- Rv3133c (devR) (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:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Citation	Characterization of a Mycobacterium smegmatis mutant lacking penicillin binding protein 1. authors,H. Billman-Jacobe,RE. Haites,RL. Coppel Antimicrob. Agents Chemother. 1999	singhpankaj2116	IDA	10582900	Band Shift
Interaction	PhysicalInteraction Rv0016c	singhpankaj2116	IDA		Band Shift authors,H. Billman-Jacobe,RE. Haites,RL. Coppel Characterization of a Mycobacterium smegmatis mutant lacking penicillin binding protein 1. Antimicrob. Agents Chemother. 1999
Citation	Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. authors,M. Strong,TG. Graeber,M. Beeby,M. Pellegrini,MJ. Thompson,TO. Yeates,D. Eisenberg Nucleic Acids Res. 2003	singhpankaj2116	IDA	14654685	Band Shift
Interaction	PhysicalInteraction Rv0016c	singhpankaj2116	IDA		Band Shift authors,M. Strong,TG. Graeber,M. Beeby,M. Pellegrini,MJ. Thompson,TO. Yeates,D. Eisenberg Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res. 2003
Citation	Unusual conformation of the SxN motif in the crystal structure of penicillin-binding protein A from Mycobacterium tuberculosis. A. Fedarovich,RA. Nicholas,C. Davies J. Mol. Biol. 2010	singhpankaj2116	IDA	20206184	Band Shift
Interaction	PhysicalInteraction Rv0016c	singhpankaj2116	IDA		Band Shift A. Fedarovich,RA. Nicholas,C. Davies Unusual conformation of the SxN motif in the crystal structure of penicillin-binding protein A from Mycobacterium tuberculosis. J. Mol. Biol. 2010
Name	Class A penicillin binding protein, bifunctional transglycosylase/transpeptidase (currrent annotation has the wrong start codon, corrected in ref. 20400545)	mjackson	IDA		Peptidoglycan assembly/maturation
Name	Class A penicillin binding protein, bifunctional transglycosylase/transpeptidase (currrent annotation has the wrong start codon, corrected in ref. 20400545)	mjackson	IMP		Peptidoglycan assembly/maturation

TB Genome Annotation Portal