DRDK_BACT7
ID DRDK_BACT7 Reviewed; 409 AA.
AC P0DTQ2;
DT 16-OCT-2019, integrated into UniProtKB/Swiss-Prot.
DT 16-OCT-2019, sequence version 1.
DT 03-AUG-2022, entry version 8.
DE RecName: Full=5-deoxyribose kinase {ECO:0000305|PubMed:30082730};
DE EC=2.7.1.- {ECO:0000269|PubMed:30082730};
DE AltName: Full=5-deoxyribose disposal kinase {ECO:0000303|PubMed:30082730};
DE AltName: Full=Methylthioribose kinase {ECO:0000305|PubMed:30082730};
DE Short=MTR kinase;
DE EC=2.7.1.100 {ECO:0000269|PubMed:30082730};
GN Name=drdK {ECO:0000303|PubMed:30082730};
GN ORFNames=HD73_0460 {ECO:0000312|EMBL:AGE76040.1};
OS Bacillus thuringiensis serovar kurstaki (strain ATCC 35866 / NRRL B-4488 /
OS HD73).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC Bacillus cereus group.
OX NCBI_TaxID=1279365;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 35866 / NRRL B-4488 / HD73;
RX PubMed=23516207; DOI=10.1128/genomea.00080-13;
RA Liu G., Song L., Shu C., Wang P., Deng C., Peng Q., Lereclus D., Wang X.,
RA Huang D., Zhang J., Song F.;
RT "Complete genome sequence of Bacillus thuringiensis subsp. kurstaki strain
RT HD73.";
RL Genome Announc. 1:E0008013-E0008013(2013).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
RP SPECIFICITY, SUBUNIT, AND PATHWAY.
RC STRAIN=HD73-20 / BGSC 4D22;
RX PubMed=30082730; DOI=10.1038/s41467-018-05589-4;
RA Beaudoin G.A.W., Li Q., Folz J., Fiehn O., Goodsell J.L., Angerhofer A.,
RA Bruner S.D., Hanson A.D.;
RT "Salvage of the 5-deoxyribose byproduct of radical SAM enzymes.";
RL Nat. Commun. 9:3105-3105(2018).
CC -!- FUNCTION: Catalyzes the ATP-dependent phosphorylation of 5-deoxyribose
CC into 5-deoxy-alpha-D-ribose 1-phosphate, as part of a 5-deoxyribose
CC salvage pathway that recycles this toxic radical SAM enzyme by-product
CC to mainstream metabolites. Is also able to catalyze the phosphorylation
CC of 5-methylthioribose into methylthioribose 1-phosphate, but this
CC enzyme may not function in methionine salvage in B.thuringiensis since
CC it exists a paralog (MtnK) present in the methionine salvage pathway
CC cluster. Does not act on 5-deoxyribulose, 2-deoxyribose, ribose,
CC fucose, fructose, fructose 6-phosphate, and glucose.
CC {ECO:0000269|PubMed:30082730}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-deoxy-D-ribose + ATP = 5-deoxy-alpha-D-ribose 1-phosphate +
CC ADP + H(+); Xref=Rhea:RHEA:61288, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:58749, ChEBI:CHEBI:149540,
CC ChEBI:CHEBI:456216; Evidence={ECO:0000269|PubMed:30082730};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:61289;
CC Evidence={ECO:0000305|PubMed:30082730};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-(methylsulfanyl)-D-ribose + ATP = ADP + H(+) + S-methyl-5-
CC thio-alpha-D-ribose 1-phosphate; Xref=Rhea:RHEA:22312,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:58533,
CC ChEBI:CHEBI:78440, ChEBI:CHEBI:456216; EC=2.7.1.100;
CC Evidence={ECO:0000269|PubMed:30082730};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=178 uM for 5-deoxy-D-ribose {ECO:0000269|PubMed:30082730};
CC KM=72 uM for S-methyl-5-thio-D-ribose {ECO:0000269|PubMed:30082730};
CC KM=216 uM for ATP {ECO:0000269|PubMed:30082730};
CC Note=kcat is 15.4 sec(-1) with 5-deoxy-D-ribose as substrate. kcat is
CC 6.2 sec(-1) with S-methyl-5-thio-D-ribose as substrate.
CC {ECO:0000269|PubMed:30082730};
CC -!- PATHWAY: Carbohydrate degradation. {ECO:0000305|PubMed:30082730}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:30082730}.
CC -!- SIMILARITY: Belongs to the methylthioribose kinase family.
CC {ECO:0000305}.
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DR EMBL; CP004069; AGE76040.1; -; Genomic_DNA.
DR RefSeq; WP_000033255.1; NC_020238.1.
DR AlphaFoldDB; P0DTQ2; -.
DR SMR; P0DTQ2; -.
DR KEGG; btt:HD73_0460; -.
DR BioCyc; MetaCyc:MON-21301; -.
DR GO; GO:0005524; F:ATP binding; IDA:UniProtKB.
DR GO; GO:0019200; F:carbohydrate kinase activity; IDA:UniProtKB.
DR GO; GO:0046522; F:S-methyl-5-thioribose kinase activity; IEA:UniProtKB-EC.
DR GO; GO:0046835; P:carbohydrate phosphorylation; IDA:UniProtKB.
DR GO; GO:0009086; P:methionine biosynthetic process; IEA:InterPro.
DR GO; GO:0110052; P:toxic metabolite repair; NAS:UniProtKB.
DR InterPro; IPR002575; Aminoglycoside_PTrfase.
DR InterPro; IPR011009; Kinase-like_dom_sf.
DR InterPro; IPR009212; Methylthioribose_kinase.
DR Pfam; PF01636; APH; 1.
DR PIRSF; PIRSF031134; MTRK; 1.
DR SUPFAM; SSF56112; SSF56112; 1.
DR TIGRFAMs; TIGR01767; MTRK; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Carbohydrate metabolism; Kinase; Nucleotide-binding;
KW Transferase.
FT CHAIN 1..409
FT /note="5-deoxyribose kinase"
FT /id="PRO_0000448255"
FT BINDING 43
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O31663"
FT BINDING 60
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O31663"
FT BINDING 113..115
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O31663"
FT BINDING 233
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O31663"
FT BINDING 250..252
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O31663"
FT BINDING 349
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O31663"
SQ SEQUENCE 409 AA; 47056 MW; 482DDE1621567FCE CRC64;
MSKFTKYFLM EASDVIAYVK EKLSKFEHAK GLKCKEIGDG NLNYVFRVWD KKENMSVIVK
QAGDTARISD EFKLSTNRIR IESDVLQLEN ELAPGLVPKV YLFDSVMNCC VMEDLSNHTI
LRTALINHQI FPQLADDLTT FMVNTLLLTS DVVMNHKEKK ELVKNYINPE LCEITEDLVY
SEPFTNHNKR NELFPLNEGW IREHIYSDKE LRMEVAKRKF SFMTNAQALL HGDLHTGSVF
VRDDSTKVID PEFAFYGPMG YDVGNVMANL MFAWVNADAT MPPGAEKDTY MDWLQTTMVE
VIDLFKKKFL DAWDIHVTEI MAKEEGFNEV YLQSVLEDTA AVTGLELIRR IVGLAKVKDI
TCIENEEARA RAEQICLKVA KSFILRANQY RTGRSFVETL KEQSMHYAE
