Rv3717 (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: N-acetylmuramoyl-L-alanine amidase
- REFSEQ: hypothetical protein
- PATRIC: probable secreted protein
- TUBERCULIST: Conserved hypothetical protein
- NCBI: hypothetical protein
- updated information (H37Rv4):
  - gene name: ami1
  - function: peptidoglycan amidase
  - reference: Healy (2020) PMID: 32127458
Type: Conditional
Start: 4161048
End: 4161773
Operon:

Trans-membrane region:
Role: II.B.4 - Polysaccharides, lipopolysaccharides and phospholipids
GO terms:
- GO:0071555 - cell wall organization (Uniprot)
- GO:0046872 - metal ion binding (Uniprot)
- GO:0042597 - periplasmic space (Uniprot)
- GO:0030288 - outer membrane-bounded periplasmic space (Uniprot)
- GO:0016998 - cell wall macromolecule catabolic process (Uniprot)
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0009253 - peptidoglycan catabolic process (Uniprot)
- GO:0008745 - N-acetylmuramoyl-L-alanine amidase 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
4M6I	100%	Mycobacterium tuberculosis	Structure of the reduced, Zn-bound form of Mycobacterium tuberculosis peptidoglycan amidase Rv3717
4M6H	100%	Mycobacterium tuberculosis	Structure of the reduced, metal-free form of Mycobacterium tuberculosis peptidoglycan amidase Rv3717
4M6G	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Structure of the Mycobacterium tuberculosis peptidoglycan amidase Rv3717 in complex with L-Alanine-iso-D-Glutamine reaction product
4LQ6	100%	Mycobacterium tuberculosis	Crystal structure of Rv3717 reveals a novel amidase from M. tuberculosis

Links to additional information on Rv3717:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.891 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MIVGVLVAAATPIISSASATPANIAGMVVFIDPGHNGANDASIGRQVPTGRGGTKNCQASGTSTNSGYPEHTFTWETGLRLRAALNALGVRTALSRGNDN
ALGPCVDERANMANALRPNAIVSLHADGGPASGRGFHVNYSAPPLNAIQAGPSVQFARIMRDQLQASGIPKANYIGQDGLYGRSDLAGLNLAQYPSILVE
LGNMKNPADSALMESAEGRQKYANALVRGVAGFLATQGQAR

(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; 4 non-insertions in a row out of 12 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 12 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 12 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 13 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 13 sites
Non-Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Non-Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 2.22
Non-Essential	7H09/7H10 + rich media	H37RvMA	MotifHMM	DeJesus et al. (2017)	Fully saturated (14 reps).

TnSeq Data

collected by: Cara Boutte (Rubin lab) (7/28/2015)
counts: delta_Rv3717_TnSeq.wig
reference: H37Rv_TnSeq.wig
resampling:resampling_H37Rv_vs_delta_Rv3717_TTR.xlsx

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:
- Rv0678 (-) (Direct binding)
- Rv1423 (whiA) (Direct binding)
- Rv1990c (-) (Direct binding)
- Rv3246c (mtrA) (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:

Property	Value	Creator	Evidence	PMID	Comment
Citation	A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. EC. Hett, MC. Chao et al. PLoS Pathog. 2008	vijayachitra	NAS	18463693	None
Interaction	Regulatory Rv3414c	vijayachitra	NAS		EC. Hett, MC. Chao et al. A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. PLoS Pathog. 2008
Citation	The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. HI. Boshoff, TG. Myers et al. J. Biol. Chem. 2004	aparna.vchalam	NAS	15247240	None
Interaction	Regulatory Rv3414c	aparna.vchalam	NAS		HI. Boshoff, TG. Myers et al. The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. J. Biol. Chem. 2004
Citation	A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. EC. Hett, MC. Chao et al. PLoS Pathog. 2008	aparna.vchalam	NAS	18463693	None
Interaction	Regulatory Rv3414c	aparna.vchalam	NAS		EC. Hett, MC. Chao et al. A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. PLoS Pathog. 2008
Citation	The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. HI. Boshoff, TG. Myers et al. J. Biol. Chem. 2004	vijayachitra	NAS	15247240	None
Interaction	Regulatory Rv3414c	vijayachitra	NAS		HI. Boshoff, TG. Myers et al. The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. J. Biol. Chem. 2004

TB Genome Annotation Portal