TB Genome Annotation Portal

Rv1379 (pyrR)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: pyrR protein
  • REFSEQ: bifunctional pyrimidine regulatory protein PyrR uracil phosphoribosyltransferase
  • PATRIC: Uracil phosphoribosyltransferase (EC 2.4.2.9) / Pyrimidine operon regulatory protein PyrR
  • TUBERCULIST: Probable pyrimidine operon regulatory protein PyrR
  • NCBI: Probable pyrimidine operon regulatory protein PyrR
  • updated information (H37Rv4):
    • gene name: pyrR
    • function:
    • reference:
• Type: Not Target
• Start: 1552654
• End: 1553235
• Operon:


• Trans-membrane region:
  
• Role: I.J.1 - Repressors/activators
• GO terms:
  • GO:0016757 - transferase activity, transferring glycosyl groups (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0009116 - nucleoside metabolic process (Uniprot)
  • GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
  • GO:0006351 - transcription, DNA-templated (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
  • GO:0004845 - uracil phosphoribosyltransferase 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: 1w30
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  5IAO	100%	Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)	Structure and mapping of spontaneous mutational sites of PyrR from Mycobacterium tuberculosis
  1W30	99%	MYCOBACTERIUM TUBERCULOSIS	PyrR of Mycobacterium Tuberculosis as a potential drug target
  4P81	58%	synthetic construct	Structure of ancestral PyrR protein (AncORANGEPyrR)
  4P3K	56%	synthetic construct	Structure of ancestral PyrR protein (PLUMPyrR)
  4P84	56%	synthetic construct	Structure of engineered PyrR protein (VIOLET PyrR)
  2IGB	55%	Bacillus caldolyticus	Crystal Structure of PyrR, The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus, UMP-bound form
  1XZN	55%	Bacillus caldolyticus	PYRR, THE REGULATOR OF THE PYRIMIDINE BIOSYNTHETIC OPERON IN BACILLUS CALDOLYTICUS, sulfate-bound form
  1XZ8	55%	Bacillus caldolyticus	Pyrr, The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus, Nucleotide-bound form
  1NON	55%	Bacillus caldolyticus	PyrR, the regulator of the pyrimidine biosynthetic operon in Bacillus caldolyticus
  4P80	54%	synthetic construct	Structure of ancestral PyrR protein (AncGREENPyrR)

• Links to additional information on pyrR:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -10.887 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MGAAGDAAIGRESRELMSAADVGRTISRIAHQIIEKTALDDPVGPDAPRVVLLGIPTRGVTLANRLAGNITEYSGIHVGHGALDITLYRDDLMIKPPRPL
ASTSIPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGRPRAVQLAVLVDRGHRELPLRADYVGKNVPTSRSESVHVRLREHDGRDGVVISR

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)	2.22 (0.51)	1.27 (0.44)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link