DRDA_BACT7
ID DRDA_BACT7 Reviewed; 213 AA.
AC P0DTQ0;
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-deoxy-D-ribulose 1-phosphate aldolase {ECO:0000305|PubMed:30082730};
DE EC=4.1.2.- {ECO:0000269|PubMed:30082730};
DE AltName: Full=5-deoxyribose disposal aldolase {ECO:0000303|PubMed:30082730};
GN Name=drdA {ECO:0000303|PubMed:30082730};
GN ORFNames=HD73_0462 {ECO:0000312|EMBL:AGE76042.1};
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] {ECO:0007744|PDB:6BTD, ECO:0007744|PDB:6BTG}
RP X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) IN COMPLEXES WITH MANGANESE AND
RP DHAP, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES,
RP COFACTOR, DISRUPTION PHENOTYPE, PATHWAY, REACTION MECHANISM, AND ACTIVE
RP SITE.
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 cleavage of 5-deoxy-D-ribulose 1-phosphate to
CC yield dihydroxyacetone phosphate (DHAP) and acetaldehyde, as part of a
CC 5-deoxyribose salvage pathway that recycles this toxic radical SAM
CC enzyme by-product to mainstream metabolites. Is also able to catalyze
CC the reverse reaction, using several aldehydes as substrate, with
CC acetaldehyde being the preferred substrate.
CC {ECO:0000269|PubMed:30082730}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-deoxy-D-ribulose 1-phosphate = acetaldehyde +
CC dihydroxyacetone phosphate; Xref=Rhea:RHEA:61300, ChEBI:CHEBI:15343,
CC ChEBI:CHEBI:57642, ChEBI:CHEBI:144504;
CC Evidence={ECO:0000269|PubMed:30082730};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:61301;
CC Evidence={ECO:0000269|PubMed:30082730};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:30082730};
CC Note=Binds 1 Mn(2+) ion per subunit. To a much lesser extent, can also
CC use Co(2+) and Mg(2+) as cofactor, but not Zn(2+).
CC {ECO:0000269|PubMed:30082730};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=36 uM for 5-deoxy-D-ribulose 1-phosphate
CC {ECO:0000269|PubMed:30082730};
CC Note=kcat is 6.3 sec(-1) for the cleavage of 5-deoxy-D-ribulose 1-
CC phosphate. {ECO:0000269|PubMed:30082730};
CC -!- PATHWAY: Carbohydrate degradation. {ECO:0000305|PubMed:30082730}.
CC -!- SUBUNIT: Forms homooligomers, possibly homotetramers.
CC {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. {ECO:0000269|PubMed:30082730}.
CC -!- SIMILARITY: Belongs to the aldolase class II family. {ECO:0000305}.
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DR EMBL; CP004069; AGE76042.1; -; Genomic_DNA.
DR RefSeq; WP_000926553.1; NC_020238.1.
DR PDB; 6BTD; X-ray; 1.55 A; A=1-213.
DR PDB; 6BTG; X-ray; 1.70 A; A=1-213.
DR PDBsum; 6BTD; -.
DR PDBsum; 6BTG; -.
DR AlphaFoldDB; P0DTQ0; -.
DR SMR; P0DTQ0; -.
DR KEGG; btt:HD73_0462; -.
DR BioCyc; MetaCyc:MON-21303; -.
DR BRENDA; 4.1.2.62; 8219.
DR GO; GO:0016832; F:aldehyde-lyase activity; IDA:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
DR GO; GO:0005975; P:carbohydrate metabolic process; IDA:UniProtKB.
DR GO; GO:0110052; P:toxic metabolite repair; IMP:UniProtKB.
DR Gene3D; 3.40.225.10; -; 1.
DR InterPro; IPR001303; Aldolase_II/adducin_N.
DR InterPro; IPR036409; Aldolase_II/adducin_N_sf.
DR Pfam; PF00596; Aldolase_II; 1.
DR SMART; SM01007; Aldolase_II; 1.
DR SUPFAM; SSF53639; SSF53639; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Manganese; Metal-binding.
FT CHAIN 1..213
FT /note="5-deoxy-D-ribulose 1-phosphate aldolase"
FT /id="PRO_0000448253"
FT ACT_SITE 76
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:30082730"
FT BINDING 28..29
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:30082730"
FT BINDING 45..46
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:30082730"
FT BINDING 74..76
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:30082730"
FT BINDING 76
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:30082730"
FT BINDING 95
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:30082730"
FT BINDING 97
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:30082730"
FT BINDING 157
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:30082730"
SQ SEQUENCE 213 AA; 23683 MW; 85A84EFA869E36BC CRC64;
MLLQKEREEI VAYGKKMISS GLTKGTGGNI SIFNREQGLV AISPSGLEYY ETKPEDVVIL
NLDGEVIEGE RKPSSELDMH LIYYRKREDI NALVHTHSPY AKTIASLGWE LPAVSYLIAF
AGPNVRCAPY ETFGTKQLAD AAFEGMIDRR AVLLANHGLI AGANNIKMAF TVAEEIEFCA
QIYYQTKSIG EPKLLPEDEM ENLAKKFEGY GQQ
