TB Genome Annotation Portal

Rv2870c (dxr)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
  • REFSEQ: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
  • PATRIC: 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267)
  • TUBERCULIST: Probable 1-deoxy-D-xylulose 5-phosphate reductoisomerase Dxr (DXP reductoisomerase) (1-deoxyxylulose-5-phosphate reductoisomerase)
  • NCBI: Probable 1-deoxy-D-xylulose 5-phosphate reductoisomerase Dxr (DXP reductoisomerase) (1-deoxyxylulose-5-phosphate reductoisomerase)
  • updated information (H37Rv4):
    • gene name: dxr
    • function:
    • reference:
• Type: Not Target
• Start: 3181770
• End: 3183011
• Operon:


• Trans-membrane region:
  
• Role: V - Conserved hypotheticals
• GO terms:
  • GO:0070402 - NADPH binding (Uniprot)
  • GO:0055114 - oxidation-reduction process (Uniprot)
  • GO:0051484 - isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process (Uniprot)
  • GO:0051483 - terpenoid biosynthetic process, mevalonate-independent (Uniprot)
  • GO:0050897 - cobalt ion binding (Uniprot)
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0030604 - 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity (Uniprot)
  • GO:0030145 - manganese ion binding (Uniprot)
  • GO:0019288 - isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway (Uniprot)
  • GO:0016491 - oxidoreductase activity (Uniprot)
  • GO:0008299 - isoprenoid biosynthetic process (Uniprot)
  • GO:0000287 - magnesium ion binding (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • NADPH[c] + DX5P[c] -> NADP[c] + MDE4P[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: 4aic, 2jcz, 2jcx, 2jcy, 2jcv, 2y1f, 2y1e, 2y1d, 2y1c, 2y1g, 3ras, 2jd2, 2jd1, 2jd0, 2c82, 4a03
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  4AIC	100%	MYCOBACTERIUM TUBERCULOSIS	X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with fosmidomycin, manganese and NADPH
  4A03	100%	MYCOBACTERIUM TUBERCULOSIS	Crystal Structure of Mycobacterium tuberculosis DXR in complex with the antibiotic FR900098 and cofactor NADPH
  3ZI0	100%	MYCOBACTERIUM TUBERCULOSIS	Structure of Mycobacterium tuberculosis DXR in complex with a fosmidomycin analogue
  3ZHZ	100%	MYCOBACTERIUM TUBERCULOSIS	Structure of Mycobacterium tuberculosis DXR in complex with a fosmidomycin analogue
  3ZHY	100%	MYCOBACTERIUM TUBERCULOSIS	Structure of Mycobacterium tuberculosis DXR in complex with a di- substituted fosmidomycin analogue
  3ZHX	100%	MYCOBACTERIUM TUBERCULOSIS	Structure of Mycobacterium tuberculosis DXR in complex with a fosmidomycin analogue
  3RAS	100%	Mycobacterium tuberculosis	Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) complexed with a lipophilic phosphonate inhibitor
  2Y1G	100%	MYCOBACTERIUM TUBERCULOSIS	X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with a 3,4- dichlorophenyl-substituted FR900098 analogue and manganese.
  2Y1F	100%	MYCOBACTERIUM TUBERCULOSIS	X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with a 3,4- dichlorophenyl-substituted fosmidomycin analogue, manganese and NADPH.
  2Y1E	100%	MYCOBACTERIUM TUBERCULOSIS	X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with manganese.

• Links to additional information on dxr:
  • 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 = -7.048 (from Jeremy Rock's lab)
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VTNSTDGRADGRLRVVVLGSTGSIGTQALQVIADNPDRFEVVGLAAGGAHLDTLLRQRAQTGVTNIAVADEHAAQRVGDIPYHGSDAATRLVEQTEADVV
LNALVGALGLRPTLAALKTGARLALANKESLVAGGSLVLRAARPGQIVPVDSEHSALAQCLRGGTPDEVAKLVLTASGGPFRGWSAADLEHVTPEQAGAH
PTWSMGPMNTLNSASLVNKGLEVIETHLLFGIPYDRIDVVVHPQSIIHSMVTFIDGSTIAQASPPDMKLPISLALGWPRRVSGAAAACDFHTASSWEFEP
LDTDVFPAVELARQAGVAGGCMTAVYNAANEEAAAAFLAGRIGFPAIVGIIADVLHAADQWAVEPATVDDVLDAQRWARERAQRAVSGMASVAIASTAKP
GAAGRHASTLERS

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)	2.05 (0.31)	1.31 (0.47)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link