DRDI_BACT7
ID DRDI_BACT7 Reviewed; 348 AA.
AC P0DTQ1;
DT 16-OCT-2019, integrated into UniProtKB/Swiss-Prot.
DT 16-OCT-2019, sequence version 1.
DT 03-AUG-2022, entry version 9.
DE RecName: Full=5-deoxyribose 1-phosphate isomerase {ECO:0000255|HAMAP-Rule:MF_02229, ECO:0000305|PubMed:30082730};
DE EC=5.3.1.- {ECO:0000255|HAMAP-Rule:MF_02229, ECO:0000269|PubMed:30082730};
DE AltName: Full=5-deoxyribose disposal isomerase {ECO:0000303|PubMed:30082730};
DE AltName: Full=Methylthioribose-1-phosphate isomerase {ECO:0000305|PubMed:30082730};
DE Short=M1Pi;
DE Short=MTR-1-P isomerase;
DE EC=5.3.1.23 {ECO:0000305|PubMed:30082730};
DE AltName: Full=S-methyl-5-thioribose-1-phosphate isomerase {ECO:0000305|PubMed:30082730};
GN Name=drdI {ECO:0000255|HAMAP-Rule:MF_02229, ECO:0000303|PubMed:30082730};
GN ORFNames=HD73_0461 {ECO:0000312|EMBL:AGE76041.1};
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, SUBUNIT,
RP PATHWAY, AND DISRUPTION PHENOTYPE.
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 isomerization of 5-deoxy-alpha-D-ribose 1-
CC phosphate to 5-deoxy-D-ribulose 1-phosphate, as part of a 5-deoxyribose
CC salvage pathway that recycles this toxic radical SAM enzyme by-product
CC to mainstream metabolites. Also seems to be able to catalyze the
CC conversion of methylthioribose-1-phosphate (MTR-1-P) into
CC methylthioribulose-1-phosphate (MTRu-1-P). However this enzyme may not
CC function in methionine salvage in B.thuringiensis since it exists a
CC paralog (MtnA) present in the methionine salvage pathway cluster.
CC {ECO:0000269|PubMed:30082730}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-deoxy-alpha-D-ribose 1-phosphate = 5-deoxy-D-ribulose 1-
CC phosphate; Xref=Rhea:RHEA:61296, ChEBI:CHEBI:58749,
CC ChEBI:CHEBI:144504; Evidence={ECO:0000255|HAMAP-Rule:MF_02229,
CC ECO:0000269|PubMed:30082730};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:61297;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02229,
CC ECO:0000269|PubMed:30082730};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-
CC D-ribulose 1-phosphate; Xref=Rhea:RHEA:19989, ChEBI:CHEBI:58533,
CC ChEBI:CHEBI:58548; EC=5.3.1.23;
CC Evidence={ECO:0000305|PubMed:30082730};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=22 mM for 5-deoxy-alpha-D-ribose 1-phosphate
CC {ECO:0000269|PubMed:30082730};
CC Note=kcat is 3.5 sec(-1) with 5-deoxy-alpha-D-ribose 1-phosphate as
CC substrate. {ECO:0000269|PubMed:30082730};
CC -!- PATHWAY: Carbohydrate degradation. {ECO:0000255|HAMAP-Rule:MF_02229,
CC ECO:0000305|PubMed:30082730}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:30082730}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene show no impaired growth
CC on minimal medium but addition of 5-deoxyribose inhibits growth at a
CC higher level than wild-type. Moreover, the intracellular level of 5-
CC deoxy-D-ribulose 1-phosphate increases in wild-type cells supplied with
CC 5-deoxyribose, but not in the deletion mutant cells.
CC {ECO:0000269|PubMed:30082730}.
CC -!- SIMILARITY: Belongs to the EIF-2B alpha/beta/delta subunits family.
CC DrdI subfamily. {ECO:0000255|HAMAP-Rule:MF_02229}.
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DR EMBL; CP004069; AGE76041.1; -; Genomic_DNA.
DR RefSeq; WP_003283000.1; NC_020238.1.
DR AlphaFoldDB; P0DTQ1; -.
DR SMR; P0DTQ1; -.
DR KEGG; btt:HD73_0461; -.
DR BioCyc; MetaCyc:MON-21302; -.
DR GO; GO:0016861; F:intramolecular oxidoreductase activity, interconverting aldoses and ketoses; IDA:UniProtKB.
DR GO; GO:0046523; F:S-methyl-5-thioribose-1-phosphate isomerase activity; IEA:UniProtKB-EC.
DR GO; GO:0005975; P:carbohydrate metabolic process; IDA:UniProtKB.
DR GO; GO:0044249; P:cellular biosynthetic process; IEA:InterPro.
DR GO; GO:0019323; P:pentose catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0110052; P:toxic metabolite repair; IMP:UniProtKB.
DR Gene3D; 1.20.120.420; -; 1.
DR Gene3D; 3.40.50.10470; -; 1.
DR HAMAP; MF_02229; Deoxyribose1P_isomerase; 1.
DR HAMAP; MF_01678; Salvage_MtnA; 1.
DR InterPro; IPR043679; Deoxyribose1P_isomerase_DrdI.
DR InterPro; IPR000649; IF-2B-related.
DR InterPro; IPR005251; IF-M1Pi.
DR InterPro; IPR042529; IF_2B-like_C.
DR InterPro; IPR011559; Initiation_fac_2B_a/b/d.
DR InterPro; IPR027363; M1Pi_N.
DR InterPro; IPR037171; NagB/RpiA_transferase-like.
DR Pfam; PF01008; IF-2B; 1.
DR SUPFAM; SSF100950; SSF100950; 1.
DR TIGRFAMs; TIGR00524; eIF-2B_rel; 1.
DR TIGRFAMs; TIGR00512; salvage_mtnA; 1.
PE 1: Evidence at protein level;
KW Carbohydrate metabolism; Isomerase.
FT CHAIN 1..348
FT /note="5-deoxyribose 1-phosphate isomerase"
FT /id="PRO_0000448254"
FT ACT_SITE 240
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02229"
FT BINDING 49..51
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02229"
FT BINDING 92
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02229"
FT BINDING 199
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02229"
FT BINDING 250..251
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02229"
FT SITE 160
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02229"
SQ SEQUENCE 348 AA; 38473 MW; 89E1175DC0539869 CRC64;
MMEEQLIPIQ WKDDALVLLD QTLLPNEIVY ESFKTAESVW DAIQVMKVRG APVIGVSAAY
GVYLGVKEFA ESTEEGFMDE VRKVCTYLAT SRPTAVNLFW ALERMESVAA DNIHLSISQL
KDRLLEEAKE IHREDEEINR QIGEHALTLF HDGMGVLTHC NAGALATTKY GTATAPMYLA
KEKGWDLKIF SDETRPRLQG STLTALELQR AGIDVTVITD NMAAMVMSQG KIDAVIVGCD
RVAANGDIAN KIGTLGVSIL AKYYNIPFYV AAPTPTIDLK TPTGKEIPIE ERDASEVINR
FGQYSAPKES KVYNPAFDVT PHENVTAIIT EKGIVKAPFT ENLKKIFQ
