Rv0670 (end)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: apurinic endonuclease (APN1)
- REFSEQ: endonuclease IV
- PATRIC: Endonuclease IV (EC 3.1.21.2)
- TUBERCULIST: Probable endonuclease IV End (endodeoxyribonuclease IV) (apurinase)
- NCBI: Probable endonuclease IV End (endodeoxyribonuclease IV) (apurinase)
- updated information (H37Rv4):
  - gene name: end
  - function:
  - reference:
Type: Not Target
Start: 769792
End: 770550
Operon:

Trans-membrane region:
Role: II.B.2 - DNA
GO terms:
- GO:0090305 - nucleic acid phosphodiester bond hydrolysis (Uniprot)
- GO:0046872 - metal ion binding (Uniprot)
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0008833 - deoxyribonuclease IV (phage-T4-induced) activity (Uniprot)
- GO:0008270 - zinc ion binding (Uniprot)
- GO:0008081 - phosphoric diester hydrolase activity (Uniprot)
- GO:0006974 - cellular response to DNA damage stimulus (Uniprot)
- GO:0006284 - base-excision repair (Uniprot)
- GO:0006281 - DNA repair (Uniprot)
- GO:0004519 - endonuclease activity (Uniprot)
- GO:0004518 - nuclease activity (Uniprot)
- GO:0003906 - DNA-(apurinic or apyrimidinic site) endonuclease activity (Uniprot)
- GO:0003677 - DNA binding (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

5ZHZ 99% Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) Crystal structure of the apurinic/apyrimidinic endonuclease IV from Mycobacterium tuberculosis
Links to additional information on end:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.856 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

PDB	aa ident	species	PDB title
5ZHZ	99%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of the apurinic/apyrimidinic endonuclease IV from Mycobacterium tuberculosis

Amino Acid Sequence

VLIGSHVSPTDPLAAAEAEGADVVQIFLGNPQSWKAPKPRDDAAALKAATLPIYVHAPYLINLASANNRVRIPSRKILQETCAAAADIGAAAVIVHGGHV
ADDNDIDKGFQRWRKALDRLETEVPVYLENTAGGDHAMARRFDTIARLWDVIGDTGIGFCLDTCHTWAAGEALTDAVDRIKAITGRIDLVHCNDSRDEAG
SGRDRHANLGSGQIDPDLLVAAVKAAGAPVICETADQGRKDDIAFLRERTGS

(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
Uncertain	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.439550; 3 non-insertions in a row out of 5 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 5 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000050; 2 non-insertions in a row out of 5 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 5 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 5 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: 0.91
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

RNA processing and modification

Energy production and conversion

Chromatin structure and dynamics

Amino acid transport and metabolism

Cell cycle control, cell division, chromosome partitioning

Carbohydrate transport and metabolism

Nucleotide transport and metabolism

Lipid transport and metabolism

Coenzyme transport and metabolism

Transcription

Translation, ribosomal structure and biogenesis

Cell wall/membrane/envelope biogenesis

Replication, recombination and repair

Posttranslational modification, protein turnover, chaperones

Cell motility

Secondary metabolites biosynthesis, transport and catabolism

Inorganic ion transport and metabolism

Function unknown

General function prediction only

Intracellular trafficking, secretion, and vesicular transport

Signal transduction mechanisms

Extracellular structures

Defense mechanisms

Nuclear structure

Cytoskeleton

BioCyc Co-regulated genes based on gene expression profiling (Systems Biology, Inferelator Network)

Differentially expressed as result of RNASeq in glycerol environment (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

Conditionally essential as result of TNSeq (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

BioCyc Transcription factor binding based on ChIP-Seq (Systems Biology)

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:
- No bindings to other targets were found.

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	Comment
Interaction	Regulatory Rv0586	sourish10	IDA	Physical Interaction MD. Santangelo, F. Blanco et al. Mce2R from Mycobacterium tuberculosis represses the expression of the mce2 operon repressor from M. tuberculosis. Tuberculosis (Edinburgh, Scotland) 2008
Interaction	Regulatory Rv0586	sourish10	IDA	Physical Interaction authors,A. Kumar,M. Bose,V. Brahmachari Analysis of expression profile of mammalian cell entry (mce) operons of Mycobacterium tuberculosis. Infect. Immun. 2003
Interaction	Regulatory Rv0586	ahal4789	IDA	Physical Interaction MD. Santangelo, F. Blanco et al. Mce2R from Mycobacterium tuberculosis represses the expression of the mce2 operon repressor from M. tuberculosis. Tuberculosis (Edinburgh, Scotland) 2008
Interaction	Regulatory Rv0586	ahal4789	IDA	Physical Interaction authors,A. Kumar,M. Bose,V. Brahmachari Analysis of expression profile of mammalian cell entry (mce) operons of Mycobacterium tuberculosis. Infect. Immun. 2003
Interaction	RegulatedBy Rv2711	yamir.moreno	TAS	Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Interaction	RegulatedBy Rv1931c	yamir.moreno	ISO	E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Interaction	RegulatedBy Rv1931c	yamir.moreno	ISO	E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. authors,M. Madan Babu,SA. Teichmann,L. Aravind Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 2006
Interaction	RegulatedBy Rv0586	yamir.moreno	IEP	LacZ-promoter fusion. expression levels of LacZ- regulated promoter fusion measured and compared between wild-type and trans-element mutation (knockout, over expression etc.). MD. Santangelo, F. Blanco et al. Mce2R from Mycobacterium tuberculosis represses the expression of the mce2 operon repressor from M. tuberculosis. Tuberculosis (Edinburgh, Scotland) 2008
Symbol	end, nfo	vmizrahi		Required for survival during early stages of infection in mice (Sassetti & Rubin, 2003).
Other	TBPWY:Base excision repair (BER)	vmizrahi		Required for survival during early stages of infection in mice (Sassetti & Rubin, 2003).

TB Genome Annotation Portal