YUTF_BACSU
ID YUTF_BACSU Reviewed; 256 AA.
AC O32125;
DT 15-DEC-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=5'-nucleotidase YutF {ECO:0000305};
DE EC=3.1.3.5 {ECO:0000269|PubMed:27907199};
GN Name=yutF; OrderedLocusNames=BSU32290;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBUNIT, INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=168;
RX PubMed=27907199; DOI=10.1371/journal.pone.0167580;
RA Zakataeva N.P., Romanenkov D.V., Yusupova Y.R., Skripnikova V.S.,
RA Asahara T., Gronskiy S.V.;
RT "Identification, heterologous expression, and functional characterization
RT of Bacillus subtilis YutF, a HAD superfamily 5'-nucleotidase with broad
RT substrate specificity.";
RL PLoS ONE 11:e0167580-e0167580(2016).
RN [3] {ECO:0007744|PDB:3PDW}
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 2-256.
RA Fedorov A.A., Fedorov E.V., Toro R., Sauder J.M., Burley S.K., Almo S.C.;
RT "Crystal structure of putative p-nitrophenyl phosphatase from Bacillus
RT subtilis.";
RL Submitted (OCT-2010) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the hydrolysis of various purine and pyrimidine 5'-
CC nucleotides, showing preference for 5'-nucleoside monophosphates and
CC exhibiting the highest catalytic activity toward 5'-XMP
CC (PubMed:27907199). Shows also a relatively high phosphohydrolase
CC activity toward the nucleotide precursors ribose-5-phosphate (R5P) and
CC 5-phosphoribosyl-1-pyrophosphate (PRPP), and toward the non-natural
CC substrate p-nitrophenyl phosphate (pNPP) (PubMed:27907199).
CC {ECO:0000269|PubMed:27907199}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-phosphate + H2O = a ribonucleoside +
CC phosphate; Xref=Rhea:RHEA:12484, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:18254, ChEBI:CHEBI:43474, ChEBI:CHEBI:58043; EC=3.1.3.5;
CC Evidence={ECO:0000269|PubMed:27907199};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + XMP = phosphate + xanthosine; Xref=Rhea:RHEA:28530,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:18107, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:57464; Evidence={ECO:0000269|PubMed:27907199};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:27907199};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.64 mM for pNPP {ECO:0000269|PubMed:27907199};
CC KM=1.53 mM for 5'-XMP {ECO:0000269|PubMed:27907199};
CC KM=1.27 mM for PRPP {ECO:0000269|PubMed:27907199};
CC KM=24 mM for R5P {ECO:0000269|PubMed:27907199};
CC KM=6.65 mM for 5'-GMP {ECO:0000269|PubMed:27907199};
CC Note=kcat is 61.0 sec(-1) with pNPP as substrate. kcat is 0.31 sec(-
CC 1) with 5'-XMP as substrate. kcat is 0.17 sec(-1) with PRPP as
CC substrate. kcat is 1.84 sec(-1) with R5P as substrate. kcat is 0.06
CC sec(-1) with 5'-GMP as substrate. {ECO:0000269|PubMed:27907199};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:27907199}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305|PubMed:27907199}.
CC -!- INDUCTION: Cotranscribed with the two upstream genes, yutD and yutE.
CC YutF overproduction increases the level of yutDEF operon expression,
CC and this up-regulation is enhanced in the presence of inorganic
CC phosphate. {ECO:0000269|PubMed:27907199}.
CC -!- DISRUPTION PHENOTYPE: Inactivation of the gene has essentially no
CC effect on cell growth in rich or minimal medium but results in a drop
CC in pNPP hydrolysis in the crude extracts of B.subtilis cells to
CC undetectable levels. {ECO:0000269|PubMed:27907199}.
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. NagD family.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AL009126; CAB15219.1; -; Genomic_DNA.
DR PIR; H70023; H70023.
DR RefSeq; NP_391109.1; NC_000964.3.
DR RefSeq; WP_003243196.1; NZ_JNCM01000033.1.
DR PDB; 3PDW; X-ray; 1.60 A; A=2-256.
DR PDBsum; 3PDW; -.
DR AlphaFoldDB; O32125; -.
DR SMR; O32125; -.
DR STRING; 224308.BSU32290; -.
DR jPOST; O32125; -.
DR PaxDb; O32125; -.
DR PRIDE; O32125; -.
DR EnsemblBacteria; CAB15219; CAB15219; BSU_32290.
DR GeneID; 936508; -.
DR KEGG; bsu:BSU32290; -.
DR PATRIC; fig|224308.179.peg.3496; -.
DR eggNOG; COG0647; Bacteria.
DR InParanoid; O32125; -.
DR OMA; PPMHRET; -.
DR PhylomeDB; O32125; -.
DR BioCyc; BSUB:BSU32290-MON; -.
DR BRENDA; 3.1.3.5; 658.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016791; F:phosphatase activity; IBA:GO_Central.
DR GO; GO:0106411; F:XMP 5'-nucleosidase activity; IEA:RHEA.
DR Gene3D; 3.40.50.1000; -; 2.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006357; HAD-SF_hydro_IIA.
DR InterPro; IPR006354; HAD-SF_hydro_IIA_hyp1.
DR InterPro; IPR023214; HAD_sf.
DR Pfam; PF13344; Hydrolase_6; 1.
DR PIRSF; PIRSF000915; PGP-type_phosphatase; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01460; HAD-SF-IIA; 1.
DR TIGRFAMs; TIGR01457; HAD-SF-IIA-hyp2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Hydrolase; Magnesium; Metal-binding;
KW Reference proteome.
FT CHAIN 1..256
FT /note="5'-nucleotidase YutF"
FT /id="PRO_0000389606"
FT STRAND 5..10
FT /evidence="ECO:0007829|PDB:3PDW"
FT STRAND 12..14
FT /evidence="ECO:0007829|PDB:3PDW"
FT HELIX 18..34
FT /evidence="ECO:0007829|PDB:3PDW"
FT STRAND 39..44
FT /evidence="ECO:0007829|PDB:3PDW"
FT HELIX 50..59
FT /evidence="ECO:0007829|PDB:3PDW"
FT HELIX 66..68
FT /evidence="ECO:0007829|PDB:3PDW"
FT STRAND 69..71
FT /evidence="ECO:0007829|PDB:3PDW"
FT HELIX 72..83
FT /evidence="ECO:0007829|PDB:3PDW"
FT STRAND 88..93
FT /evidence="ECO:0007829|PDB:3PDW"
FT HELIX 95..103
FT /evidence="ECO:0007829|PDB:3PDW"
FT STRAND 114..118
FT /evidence="ECO:0007829|PDB:3PDW"
FT HELIX 126..137
FT /evidence="ECO:0007829|PDB:3PDW"
FT STRAND 141..145
FT /evidence="ECO:0007829|PDB:3PDW"
FT STRAND 150..153
FT /evidence="ECO:0007829|PDB:3PDW"
FT STRAND 156..159
FT /evidence="ECO:0007829|PDB:3PDW"
FT HELIX 161..172
FT /evidence="ECO:0007829|PDB:3PDW"
FT HELIX 185..194
FT /evidence="ECO:0007829|PDB:3PDW"
FT HELIX 198..200
FT /evidence="ECO:0007829|PDB:3PDW"
FT STRAND 201..206
FT /evidence="ECO:0007829|PDB:3PDW"
FT TURN 208..210
FT /evidence="ECO:0007829|PDB:3PDW"
FT HELIX 211..218
FT /evidence="ECO:0007829|PDB:3PDW"
FT STRAND 221..225
FT /evidence="ECO:0007829|PDB:3PDW"
FT STRAND 243..248
FT /evidence="ECO:0007829|PDB:3PDW"
FT HELIX 249..252
FT /evidence="ECO:0007829|PDB:3PDW"
FT HELIX 253..256
FT /evidence="ECO:0007829|PDB:3PDW"
SQ SEQUENCE 256 AA; 27957 MW; DB8C03D073AA1AD2 CRC64;
MKTYKGYLID LDGTMYNGTE KIEEACEFVR TLKDRGVPYL FVTNNSSRTP KQVADKLVSF
DIPATEEQVF TTSMATAQHI AQQKKDASVY VIGEEGIRQA IEENGLTFGG ENADFVVVGI
DRSITYEKFA VGCLAIRNGA RFISTNGDIA IPTERGLLPG NGSLTSVLTV STGVQPVFIG
KPESIIMEQA MRVLGTDVSE TLMVGDNYAT DIMAGINAGM DTLLVHTGVT KREHMTDDME
KPTHAIDSLT EWIPYI
