Rv3601c (panD)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: aspartate 1-decarboxylase
- REFSEQ: aspartate alpha-decarboxylase
- PATRIC: Aspartate 1-decarboxylase (EC 4.1.1.11)
- TUBERCULIST: Probable aspartate 1-decarboxylase precursor PanD (aspartate alpha-decarboxylase)
- NCBI: Probable aspartate 1-decarboxylase precursor PanD (aspartate alpha-decarboxylase)
- updated information (H37Rv4):
  - gene name: panD
  - function:
  - reference:
Type: Not Target
Start: 4043862
End: 4044281
Operon:

Trans-membrane region:
Role: I.G.5 - Pantothenate
GO terms:
- GO:0016831 - carboxy-lyase activity (Uniprot)
- GO:0016829 - lyase activity (Uniprot)
- GO:0015940 - pantothenate biosynthetic process (Uniprot)
- GO:0009405 - pathogenesis (Uniprot)
- GO:0006523 - alanine biosynthetic process (Uniprot)
- GO:0005829 - cytosol (Uniprot)
- GO:0005737 - cytoplasm (Uniprot)
- GO:0005618 - cell wall (Uniprot)
- GO:0004068 - aspartate 1-decarboxylase activity (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- ASP[c] -> CO2[c] + bALA[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: 2c45
Search for Homologs in PDB

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

PDB	aa ident	species	PDB title
6P1Y	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mtb aspartate decarboxylase mutant M117I
6P02	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mtb aspartate decarboxylase, 6-Chlorine pyrazinoic acid complex
6P02	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mtb aspartate decarboxylase, 6-Chlorine pyrazinoic acid complex
6OZ8	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mtb aspartate decarboxylase in active form
6OZ8	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mtb aspartate decarboxylase in active form
6OYY	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mtb aspartate decarboxylase, pyrazinoic acid complex
6OYY	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mtb aspartate decarboxylase, pyrazinoic acid complex
2C45	100%	Mycobacterium tuberculosis	NATIVE PRECURSOR OF PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE
6P1Y	99%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mtb aspartate decarboxylase mutant M117I
2EEO	63%	Thermus thermophilus	Crystal Structure of T.th. HB8 L-Aspartate-alpha-Decarboxylase Complexed with Fumarate

Links to additional information on panD:
- KEGG - nucleotide and amino acid sequences of gene
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -4.065 (from Jeremy Rock's lab)
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MLRTMLKSKIHRATVTCADLHYVGSVTIDADLMDAADLLEGEQVTIVDIDNGARLVTYAITGERGSGVIGINGAAAHLVHPGDLVILIAYATMDDARART
YQPRIVFVDAYNKPIDMGHDPAFVPENAGELLDPRLGVG

(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: 0.978150; 8 non-insertions in a row out of 9 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.999550; 9 non-insertions in a row out of 9 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.998050; 8 non-insertions in a row out of 9 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.998050; 9 non-insertions in a row out of 10 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.999600; 10 non-insertions in a row out of 10 sites
No-Data	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Too-Short	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: -1
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:
- Rv3058c (-)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0678 (-) (Direct binding)
- Rv1033c (trcR) (Direct binding)
- Rv2642 (-) (Direct binding)
- Rv0135c (-) (Upstream of operon)
- Rv1353c (-) (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:
- Rv3058c (-)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	RegulatedBy Rv0981	yamir.moreno	IEP		Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments.. H. He, R. Hovey et al. MprAB is a stress-responsive two-component system that directly regulates expression of sigma factors SigB and SigE in Mycobacterium tuberculosis. J. Bacteriol. 2006
Citation	3-Fluoroaspartate and pyruvoyl-dependant aspartate decarboxylase: exploiting the unique characteristics of fluorine to probe reactivity and binding. authors,J. de Villiers,L. Koekemoer,E. Strauss Chemistry 2010	jevans		20645337	Not inhibited by fluorinated substrate analogues
Citation	A pantothenate auxotroph of Mycobacterium tuberculosis is highly attenuated and protects mice against tuberculosis. authors,VK. Sambandamurthy,X. Wang,B. Chen,RG. Russell,S. Derrick,FM. Collins,SL. Morris,WR. Jacobs Nat. Med. 2002	jjmcfadden		12219086	Inferred from direct assay
Term	EC:4.1.1.11 Aspartate 1-decarboxylase. - NR	jjmcfadden	NR		Inferred from direct assay authors,VK. Sambandamurthy,X. Wang,B. Chen,RG. Russell,S. Derrick,FM. Collins,SL. Morris,WR. Jacobs A pantothenate auxotroph of Mycobacterium tuberculosis is highly attenuated and protects mice against tuberculosis. Nat. Med. 2002

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