TB Genome Annotation Portal

Rv3048c (nrdF2)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: ribonucleoside-diphosphate reductase subunit beta nrdF2
  • REFSEQ: ribonucleotide-diphosphate reductase subunit beta
  • PATRIC: Ribonucleotide reductase of class Ib (aerobic) beta subunit (EC 1.17.4.1)
  • TUBERCULIST: Ribonucleoside-diphosphate reductase (beta chain) NrdF2 (ribonucleotide reductase small subunit) (R2F protein)
  • NCBI: Ribonucleoside-diphosphate reductase (beta chain) NrdF2 (ribonucleotide reductase small subunit) (R2F protein)
  • updated information (H37Rv4):
    • gene name: nrdF2
    • function:
    • reference:
• Type: Not Target
• Start: 3408404
• End: 3409378
• Operon:


• Trans-membrane region:
  
• Role: I.F.3 - 2'-deoxyribonucleotide metabolism
• GO terms:
  • GO:0055114 - oxidation-reduction process (Uniprot)
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0016491 - oxidoreductase activity (Uniprot)
  • GO:0009263 - deoxyribonucleotide biosynthetic process (Uniprot)
  • GO:0006260 - DNA replication (Uniprot)
  • GO:0005971 - ribonucleoside-diphosphate reductase complex (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
  • GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • O2[c] + RTHIO[c] + CDP[c] -> OTHIO[c] + DCDP[c]
  • UDP[c] + O2[c] + RTHIO[c] -> OTHIO[c] + DUDP[c]
  • ADP[c] + O2[c] + RTHIO[c] -> OTHIO[c] + DADP[c]
  • GDP[c] + O2[c] + RTHIO[c] -> OTHIO[c] + DGDP[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: 1uzr
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  1UZR	99%	MYCOBACTERIUM TUBERCULOSIS	Crystal Structure of the Class Ib Ribonucleotide Reductase R2F-2 subunit from Mycobacterium tuberculosis
  3DHZ	75%	Corynebacterium ammoniagenes	Apo (iron free) structure of C. ammoniagenes R2 protein
  1OQU	75%	Corynebacterium ammoniagenes	A protein coordinated tri-nuclear Fe complex formed during soaking of crystals of the ribonucleotide reductase R2F protein from Corynebacterium Ammoniagenes
  1KGP	75%	Corynebacterium ammoniagenes	R2F from Corynebacterium Ammoniagenes in its Mn substituted form
  1KGO	75%	Corynebacterium ammoniagenes	R2F from Corynebacterium Ammoniagenes in its reduced, Fe containing, form
  1KGN	75%	Corynebacterium ammoniagenes	R2F from Corynebacterium Ammoniagenes in its oxidised, Fe containing, form
  3MJO	73%	Corynebacterium ammoniagenes	Small subunit (R2F) of native ribonucleotide reductase from Corynebacterium ammoniagenes
  2R2F	71%	Salmonella typhimurium	RIBONUCLEOTIDE REDUCTASE R2F PROTEIN FROM SALMONELLA TYPHIMURIUM (OXIDIZED)
  2BQ1	71%	SALMONELLA TYPHIMURIUM	Ribonucleotide reductase class 1b holocomplex R1E,R2F from Salmonella typhimurium
  1R2F	71%	Salmonella typhimurium	RIBONUCLEOTIDE REDUCTASE R2F PROTEIN FROM SALMONELLA TYPHIMURIUM

• Links to additional information on nrdF2:
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -5.566 (from Jeremy Rock's lab)

Amino Acid Sequence

VTGNAKLIDRVSAINWNRLQDEKDAEVWDRLTGNFWLPEKVPVSNDIPSWGTLTAGEKQLTMRVFTGLTMLDTIQGTVGAVSLIPDALTPHEEAVLTNIA
FMESVHAKSYSQIFSTLCSTAEIDDAFRWSEENRNLQRKAEIVLQYYRGDEPLKRKVASTLLESFLFYSGFYLPMYWSSRAKLTNTADMIRLIIRDEAVH
GYYIGYKFQRGLALVDDVTRAELKDYTYELLFELYDNEVEYTQDLYDEVGLTEDVKKFLRYNANKALMNLGYEALFPRDETDVNPAILSALSPNADENHD
FFSGSGSSYVIGKAVVTEDDDWDF

Additional Information