TB Genome Annotation Portal

Rv1338 (murI)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: glutamate racemase
  • REFSEQ: glutamate racemase
  • PATRIC: Glutamate racemase (EC 5.1.1.3)
  • TUBERCULIST: Probable glutamate racemase MurI
  • NCBI: Probable glutamate racemase MurI
  • updated information (H37Rv4):
    • gene name: murI
    • function:
    • reference: Prosser (2016) PMID: 27480853
• Type: Not Target
• Start: 1505075
• End: 1505890
• Operon:


• Trans-membrane region:
  
• Role: II.C.3 - Murein sacculus and peptidoglycan
• GO terms:
  • GO:2000372 - negative regulation of DNA topoisomerase (ATP-hydrolyzing) activity (Uniprot)
  • GO:0071555 - cell wall organization (Uniprot)
  • GO:0036361 - racemase activity, acting on amino acids and derivatives (Uniprot)
  • GO:0016855 - racemase and epimerase activity, acting on amino acids and derivatives (Uniprot)
  • GO:0016853 - isomerase activity (Uniprot)
  • GO:0009252 - peptidoglycan biosynthetic process (Uniprot)
  • GO:0008881 - glutamate racemase activity (Uniprot)
  • GO:0008657 - DNA topoisomerase (ATP-hydrolyzing) inhibitor activity (Uniprot)
  • GO:0008360 - regulation of cell shape (Uniprot)
  • GO:0008152 - metabolic process (Uniprot)
  • GO:0006807 - nitrogen compound metabolic process (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • GLU[c] -> DGLU[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:
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  5HJ7	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Glutamate Racemase Mycobacterium tuberculosis (MurI) with bound D-glutamate, 2.3 Angstrom resolution, X-ray diffraction
  5IJW	86%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Glutamate Racemase (MurI) from Mycobacterium smegmatis with bound D-glutamate, 1.8 Angstrom resolution, X-ray diffraction
  6DLI	45%	Thermus thermophilus	Crystal structure of glutamate racemase from Thermus thermophilus in complex with Beta-chloro-D-alanine
  5W16	45%	Thermus thermophilus	Crystal structure of glutamate racemase from Thermus thermophilus in complex with D-glutamate
  1ZUW	42%	Bacillus subtilis	Crystal structure of B.subtilis glutamate racemase (RacE) with D-Glu
  3ISV	42%	Listeria monocytogenes	Crystal structure of glutamate racemase from Listeria monocytogenes in complex with acetate ion
  3IST	42%	Listeria monocytogenes	Crystal structure of glutamate racemase from Listeria monocytogenes in complex with succinic acid
  3HFR	42%	Listeria monocytogenes	Crystal structure of glutamate racemase from Listeria monocytogenes
  2DWU	42%	Bacillus anthracis	Crystal Structure of Glutamate Racemase Isoform RacE1 from Bacillus anthracis
  2VVT	41%	ENTEROCOCCUS FAECALIS	Glutamate Racemase (MurI) from E. faecalis in complex with a 9-Benzyl Purine inhibitor

• Links to additional information on murI:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -8.142 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MNSPLAPVGVFDSGVGGLTVARAIIDQLPDEDIVYVGDTGNGPYGPLTIPEIRAHALAIGDDLVGRGVKALVIACNSASSACLRDARERYQVPVVEVILP
AVRRAVAATRNGRIGVIGTRATITSHAYQDAFAAARDTEITAVACPRFVDFVERGVTSGRQVLGLAQGYLEPLQRAEVDTLVLGCTHYPLLSGLIQLAMG
ENVTLVSSAEETAKEVVRVLTEIDLLRPHDAPPATRIFEATGDPEAFTKLAARFLGPVLGGVQPVHPSRIH

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)	1.41 (0.22)	1.24 (0.6)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link