RIBX_BACTN
ID RIBX_BACTN Reviewed; 206 AA.
AC Q8A947;
DT 24-JUN-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=D-ribitol-5-phosphate phosphatase {ECO:0000305|PubMed:25513739};
DE EC=3.1.3.- {ECO:0000269|PubMed:25513739};
DE AltName: Full=5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase {ECO:0000305|PubMed:25513739};
DE EC=3.1.3.104 {ECO:0000269|PubMed:25513739};
GN OrderedLocusNames=BT_0970 {ECO:0000312|EMBL:AAO76077.1};
OS Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 /
OS CCUG 10774 / NCTC 10582 / VPI-5482 / E50).
OC Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae;
OC Bacteroides.
OX NCBI_TaxID=226186;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 /
RC VPI-5482 / E50;
RX PubMed=12663928; DOI=10.1126/science.1080029;
RA Xu J., Bjursell M.K., Himrod J., Deng S., Carmichael L.K., Chiang H.C.,
RA Hooper L.V., Gordon J.I.;
RT "A genomic view of the human-Bacteroides thetaiotaomicron symbiosis.";
RL Science 299:2074-2076(2003).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND PATHWAY.
RX PubMed=25513739; DOI=10.1021/bi501140k;
RA London N., Farelli J.D., Brown S.D., Liu C., Huang H., Korczynska M.,
RA Al-Obaidi N.F., Babbitt P.C., Almo S.C., Allen K.N., Shoichet B.K.;
RT "Covalent docking predicts substrates for haloalkanoate dehalogenase
RT superfamily phosphatases.";
RL Biochemistry 54:528-537(2015).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS).
RG Enzyme Function Initiative (EFI);
RA Vetting M.W., Toro R., Bhosle R., Kumar P.R., Ghosh A., Al Obaidi N.F.,
RA Stead M., Washington E., Scott Glenn A., Chowdhury S., Evans B.,
RA Hammonds J., Hillerich B., Love J., Seidel R.D., Imker H.J.,
RA Dunaway-Mariano D., Allen K.N., Gerlt J.A., Almo S.C.;
RT "Crystal structure of BT_0970, a had family phosphatase from Bacteroides
RT thetaiotaomicron VPI-5482, TARGET EFI-501083, with bound sodium and
RT glycerol, closed lid, ordered loop.";
RL Submitted (FEB-2013) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the dephosphorylation of D-ribitol-5-phosphate and
CC D-ribitol-1-phosphate. Is also able to dephosphorylate 5-amino-6-(5-
CC phospho-D-ribitylamino)uracil, and thus could be involved in the
CC riboflavin biosynthesis pathway. {ECO:0000269|PubMed:25513739}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-ribitol 1-phosphate + H2O = phosphate + ribitol;
CC Xref=Rhea:RHEA:47652, ChEBI:CHEBI:15377, ChEBI:CHEBI:15963,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:87817;
CC Evidence={ECO:0000269|PubMed:25513739};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-ribitol 5-phosphate + H2O = phosphate + ribitol;
CC Xref=Rhea:RHEA:47648, ChEBI:CHEBI:15377, ChEBI:CHEBI:15963,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57695;
CC Evidence={ECO:0000269|PubMed:25513739};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-amino-6-(5-phospho-D-ribitylamino)uracil + H2O = 5-amino-6-
CC (D-ribitylamino)uracil + phosphate; Xref=Rhea:RHEA:25197,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15934, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:58421; EC=3.1.3.104;
CC Evidence={ECO:0000269|PubMed:25513739};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P0A8Y3};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1030 uM for D-ribitol-1-phosphate {ECO:0000269|PubMed:25513739};
CC KM=1080 uM for D-ribitol-5-phosphate {ECO:0000269|PubMed:25513739};
CC KM=102.5 uM for 5-amino-6-(5-phospho-D-ribitylamino)uracil
CC {ECO:0000269|PubMed:25513739};
CC Note=kcat is 1.8 sec(-1) with D-ribitol-1-phosphate as substrate.
CC kcat is 1.5 sec(-1) with D-ribitol-5-phosphate as substrate. kcat is
CC 0.016 sec(-1) with 5-amino-6-(5-phospho-D-ribitylamino)uracil as
CC substrate. {ECO:0000269|PubMed:25513739};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 4/4. {ECO:0000305|PubMed:25513739}.
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily.
CC {ECO:0000305}.
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DR EMBL; AE015928; AAO76077.1; -; Genomic_DNA.
DR RefSeq; NP_809883.1; NC_004663.1.
DR RefSeq; WP_008761607.1; NZ_UYXG01000013.1.
DR PDB; 4JB3; X-ray; 1.50 A; A=1-206.
DR PDBsum; 4JB3; -.
DR AlphaFoldDB; Q8A947; -.
DR SMR; Q8A947; -.
DR STRING; 226186.BT_0970; -.
DR PaxDb; Q8A947; -.
DR PRIDE; Q8A947; -.
DR DNASU; 1073603; -.
DR EnsemblBacteria; AAO76077; AAO76077; BT_0970.
DR GeneID; 60926946; -.
DR KEGG; bth:BT_0970; -.
DR PATRIC; fig|226186.12.peg.986; -.
DR eggNOG; COG1011; Bacteria.
DR HOGENOM; CLU_045011_9_5_10; -.
DR InParanoid; Q8A947; -.
DR OMA; IWIMSDT; -.
DR BRENDA; 3.1.3.104; 709.
DR UniPathway; UPA00275; UER00403.
DR Proteomes; UP000001414; Chromosome.
DR GO; GO:0043726; F:5-amino-6-(5-phosphoribitylamino)uracil phosphatase activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0110130; F:ribitol-5-phosphatase activity; IEA:RHEA.
DR GO; GO:0016311; P:dephosphorylation; IDA:UniProtKB.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IGC:UniProtKB.
DR Gene3D; 1.10.150.240; -; 1.
DR Gene3D; 3.40.50.1000; -; 1.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006439; HAD-SF_hydro_IA.
DR InterPro; IPR041492; HAD_2.
DR InterPro; IPR023214; HAD_sf.
DR InterPro; IPR023198; PGP-like_dom2.
DR Pfam; PF13419; HAD_2; 1.
DR PRINTS; PR00413; HADHALOGNASE.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01509; HAD-SF-IA-v3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..206
FT /note="D-ribitol-5-phosphate phosphatase"
FT /id="PRO_0000433304"
FT ACT_SITE 8
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P0A8Y3"
FT BINDING 8
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 172
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT STRAND 4..7
FT /evidence="ECO:0007829|PDB:4JB3"
FT TURN 11..13
FT /evidence="ECO:0007829|PDB:4JB3"
FT HELIX 18..27
FT /evidence="ECO:0007829|PDB:4JB3"
FT HELIX 33..36
FT /evidence="ECO:0007829|PDB:4JB3"
FT HELIX 44..50
FT /evidence="ECO:0007829|PDB:4JB3"
FT HELIX 56..67
FT /evidence="ECO:0007829|PDB:4JB3"
FT HELIX 73..81
FT /evidence="ECO:0007829|PDB:4JB3"
FT HELIX 89..98
FT /evidence="ECO:0007829|PDB:4JB3"
FT TURN 99..101
FT /evidence="ECO:0007829|PDB:4JB3"
FT STRAND 102..108
FT /evidence="ECO:0007829|PDB:4JB3"
FT HELIX 112..118
FT /evidence="ECO:0007829|PDB:4JB3"
FT HELIX 121..123
FT /evidence="ECO:0007829|PDB:4JB3"
FT HELIX 130..133
FT /evidence="ECO:0007829|PDB:4JB3"
FT STRAND 134..139
FT /evidence="ECO:0007829|PDB:4JB3"
FT HELIX 140..143
FT /evidence="ECO:0007829|PDB:4JB3"
FT HELIX 150..160
FT /evidence="ECO:0007829|PDB:4JB3"
FT HELIX 164..166
FT /evidence="ECO:0007829|PDB:4JB3"
FT STRAND 167..170
FT /evidence="ECO:0007829|PDB:4JB3"
FT HELIX 174..182
FT /evidence="ECO:0007829|PDB:4JB3"
FT STRAND 186..188
FT /evidence="ECO:0007829|PDB:4JB3"
FT HELIX 197..204
FT /evidence="ECO:0007829|PDB:4JB3"
SQ SEQUENCE 206 AA; 23545 MW; 615D8B01997FEA86 CRC64;
MIKNIVFDFG GVIVDIDRDK AVQAFIKLGL ADADTRLDKY HQTGIFQELE EGKLSADEFR
KQLGDLCGRE LTMEETKQAW LGFFNEVDLR KLDYILGLRK SYHVYLLSNT NPFVMSWACS
PEFSSEGKPL NDYCDKLYLS YQLGHTKPAP EIFDFMIKDS HVIPSETLFV DDGSSNIHIG
KELGFETFQP ENGADWRQEL TVILNS
