ID   PYNA_STRR6              Reviewed;         237 AA.
AC   Q8DPQ3;
DT   07-APR-2021, integrated into UniProtKB/Swiss-Prot.
DT   01-MAR-2003, sequence version 1.
DT   07-APR-2021, entry version 96.
DE   RecName: Full=Pyrimidine 5'-nucleotidase PynA {ECO:0000303|PubMed:31437335};
DE            EC=3.1.3.5 {ECO:0000269|PubMed:31437335};
DE   AltName: Full=Antimutator protein PynA {ECO:0000303|PubMed:31437335};
DE   AltName: Full=House-cleaning nucleotidase {ECO:0000303|PubMed:31437335};
DE   AltName: Full=Non-canonical pyrimidine nucleotide phosphatase {ECO:0000305};
DE   AltName: Full=Nucleoside 5'-monophosphate phosphohydrolase {ECO:0000305};
DE   AltName: Full=Pyrimidine nucleotidase A {ECO:0000303|PubMed:31437335};
DE   AltName: Full=Ribonucleotide monophosphatase {ECO:0000305};
GN   Name=pynA {ECO:0000303|PubMed:31437335};
GN   OrderedLocusNames=spr1057 {ECO:0000312|EMBL:AAK99861.1};
OS   Streptococcus pneumoniae (strain ATCC BAA-255 / R6).
OC   Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC   Streptococcus.
OX   NCBI_TaxID=171101 {ECO:0000312|EMBL:AAK99861.1};
RN   [1] {ECO:0000312|EMBL:AAK99861.1, ECO:0000312|Proteomes:UP000000586}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-255 / R6 {ECO:0000312|Proteomes:UP000000586};
RX   PubMed=11544234; DOI=10.1128/jb.183.19.5709-5717.2001;
RA   Hoskins J., Alborn W.E. Jr., Arnold J., Blaszczak L.C., Burgett S.,
RA   DeHoff B.S., Estrem S.T., Fritz L., Fu D.-J., Fuller W., Geringer C.,
RA   Gilmour R., Glass J.S., Khoja H., Kraft A.R., Lagace R.E., LeBlanc D.J.,
RA   Lee L.N., Lefkowitz E.J., Lu J., Matsushima P., McAhren S.M., McHenney M.,
RA   McLeaster K., Mundy C.W., Nicas T.I., Norris F.H., O'Gara M., Peery R.B.,
RA   Robertson G.T., Rockey P., Sun P.-M., Winkler M.E., Yang Y.,
RA   Young-Bellido M., Zhao G., Zook C.A., Baltz R.H., Jaskunas S.R.,
RA   Rosteck P.R. Jr., Skatrud P.L., Glass J.I.;
RT   "Genome of the bacterium Streptococcus pneumoniae strain R6.";
RL   J. Bacteriol. 183:5709-5717(2001).
RN   [2]
RP   FUNCTION, SUBSTRATE SPECIFICITY, CATALYTIC ACTIVITY, COFACTOR,
RP   BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, SUBCELLULAR LOCATION, AND
RP   DISRUPTION PHENOTYPE.
RC   STRAIN=Rx1 {ECO:0000303|PubMed:31437335};
RX   PubMed=31437335; DOI=10.1111/febs.15049;
RA   Ulrych A., Petrackova D., Goldova J., Buriankova K., Doubravova L.,
RA   Branny P.;
RT   "PynA is a pyrimidine 5'-nucleotidase that functions as an antimutator
RT   protein in Streptococcus pneumoniae.";
RL   FEBS J. 287:267-283(2020).
CC   -!- FUNCTION: Nucleotidase that shows high phosphatase activity toward non-
CC       canonical pyrimidine nucleotides and three canonical nucleoside 5'-
CC       monophosphates (UMP, dUMP and dTMP), and no activity against IMP, UDP,
CC       GMP, AMP, UTP or pNPP. Appears to function as a house-cleaning
CC       nucleotidase in vivo, since the general nucleotidase activity of it
CC       allows it to protect cells against non-canonical pyrimidine derivatives
CC       such as 5-fluoro-2'-deoxyuridine monophosphate (5-FdUMP), and prevents
CC       the incorporation of potentially mutagenic nucleotides such as 5-bromo-
CC       2'-deoxyuridine (5-BrdU) into DNA. Is strictly specific to pyrimidine
CC       substrates with 5'-monophosphates and shows no activity against
CC       nucleoside di- and triphosphates. {ECO:0000269|PubMed:31437335}.
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:31437335};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000269|PubMed:31437335};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000269|PubMed:31437335};
CC       Note=Strict requirement of divalent metal cation. The highest activity
CC       is observed with combination of Mg(2+) and Mn(2+), followed by Mg(2+) >
CC       Mn(2+) > Co(2+). No activity detected with Ca(2+), Cu(2+) or Zn(2+).
CC       {ECO:0000269|PubMed:31437335};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=0.29 mM for 5-fluoro-2'-deoxyuridine monophosphate (5-FdUMP) (at
CC         pH 7.5 and 37 degrees Celsius) {ECO:0000269|PubMed:31437335};
CC         KM=2.6 mM for dTMP (at pH 7.5 and 37 degrees Celsius)
CC         {ECO:0000269|PubMed:31437335};
CC         KM=2.6 mM for UMP (at pH 7.5 and 37 degrees Celsius)
CC         {ECO:0000269|PubMed:31437335};
CC         KM=2.5 mM for dUMP (at pH 7.5 and 37 degrees Celsius)
CC         {ECO:0000269|PubMed:31437335};
CC         Vmax=16.7 umol/min/mg enzyme with 5-FdUMP as substrate (at pH 7.5 and
CC         37 degrees Celsius) {ECO:0000269|PubMed:31437335};
CC         Vmax=15.1 umol/min/mg enzyme with dTMP as substrate (at pH 7.5 and 37
CC         degrees Celsius) {ECO:0000269|PubMed:31437335};
CC         Vmax=6.4 umol/min/mg enzyme with UMP as substrate (at pH 7.5 and 37
CC         degrees Celsius) {ECO:0000269|PubMed:31437335};
CC         Vmax=5.7 umol/min/mg enzyme with dUMP as substrate (at pH 7.5 and 37
CC         degrees Celsius) {ECO:0000269|PubMed:31437335};
CC         Note=kcat is 7.5 sec(-1) with 5-FdUMP as substrate (at pH 7.5 and 37
CC         degrees Celsius). kcat is 6.8 sec(-1) with dTMP as substrate (at pH
CC         7.5 and 37 degrees Celsius). kcat is 2.9 sec(-1) with UMP as
CC         substrate (at pH 7.5 and 37 degrees Celsius). kcat is 2.5 sec(-1)
CC         with dUMP as substrate (at pH 7.5 and 37 degrees Celsius). The
CC         catalytic efficiency is 10-fold higher with 5-FdUMP than with 5'-dTMP
CC         as substrate. {ECO:0000269|PubMed:31437335};
CC       pH dependence:
CC         Optimum pH is 7.5. {ECO:0000269|PubMed:31437335};
CC   -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:31437335}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:31437335}.
CC   -!- DISRUPTION PHENOTYPE: Cells lacking this gene are viable, have normal
CC       growth and morphological appearance under standard cultivation
CC       conditions, but have high sensitivity to toxic non-canonical pyrimidine
CC       derivatives such as 5-fluoro-2'-deoxyuridine (5-FdU); the growth is
CC       completely blocked by 2 uM 5-FdU. Upon exposure to mutagenic agent 5-
CC       bromo-2'-deoxyuridine (5-BrdU), 5-BrdU is extensively incorporated into
CC       the DNA and results in accumulation of random mutations with high
CC       frequency, which affect growth or generation of lethal mutations in
CC       essential genes. A 30-fold increase in the mutation rate is observed.
CC       In the presence of 5-BrdU, the cells exhibit frequent morphological
CC       abnormalities, including irregular cell shape, heterogeneous cell size
CC       and the occurrence of cells undergoing lysis.
CC       {ECO:0000269|PubMed:31437335}.
CC   -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. YjjG family.
CC       {ECO:0000305}.
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DR   EMBL; AE007317; AAK99861.1; -; Genomic_DNA.
DR   PIR; A99004; A99004.
DR   RefSeq; NP_358651.1; NC_003098.1.
DR   RefSeq; WP_000499433.1; NC_003098.1.
DR   SMR; Q8DPQ3; -.
DR   STRING; 171101.spr1057; -.
DR   EnsemblBacteria; AAK99861; AAK99861; spr1057.
DR   GeneID; 60234467; -.
DR   KEGG; spr:spr1057; -.
DR   PATRIC; fig|171101.6.peg.1149; -.
DR   eggNOG; COG1011; Bacteria.
DR   HOGENOM; CLU_045011_8_1_9; -.
DR   OMA; DHTLWDF; -.
DR   BioCyc; SPNE171101:SPR1057-MONOMER; -.
DR   Proteomes; UP000000586; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR   GO; GO:0002953; F:5'-deoxynucleotidase activity; IDA:UniProtKB.
DR   GO; GO:0008253; F:5'-nucleotidase activity; IDA:UniProtKB.
DR   GO; GO:0000287; F:magnesium ion binding; ISS:UniProtKB.
DR   GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR   GO; GO:0009159; P:deoxyribonucleoside monophosphate catabolic process; IDA:UniProtKB.
DR   GO; GO:0016311; P:dephosphorylation; IDA:UniProtKB.
DR   GO; GO:0009222; P:pyrimidine ribonucleotide catabolic process; IDA: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; IPR011951; HAD-SF_hydro_IA_YjjG/YfnB.
DR   InterPro; IPR041492; HAD_2.
DR   InterPro; IPR023214; HAD_sf.
DR   InterPro; IPR023198; PGP-like_dom2.
DR   Pfam; PF13419; HAD_2; 1.
DR   SUPFAM; SSF56784; SSF56784; 1.
DR   TIGRFAMs; TIGR01549; HAD-SF-IA-v1; 1.
DR   TIGRFAMs; TIGR02254; YjjG/YfnB; 1.
PE   1: Evidence at protein level;
KW   Cytoplasm; Hydrolase; Magnesium; Manganese; Metal-binding;
KW   Nucleotide-binding; Reference proteome.
FT   CHAIN           1..237
FT                   /note="Pyrimidine 5'-nucleotidase PynA"
FT                   /id="PRO_0000452172"
FT   ACT_SITE        9
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000250|UniProtKB:P95649"
FT   ACT_SITE        11
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000250|UniProtKB:P95649"
FT   METAL           9
FT                   /note="Magnesium"
FT                   /evidence="ECO:0000250|UniProtKB:P95649"
FT   METAL           11
FT                   /note="Magnesium; via carbonyl oxygen"
FT                   /evidence="ECO:0000250|UniProtKB:P95649"
FT   METAL           181
FT                   /note="Magnesium"
FT                   /evidence="ECO:0000250|UniProtKB:P95649"
SQ   SEQUENCE   237 AA;  27180 MW;  3FEE5E114D42EBD0 CRC64;
     MFYKFLLFDL DHTLLDFDAA EDVALTQLLK EEGVADIQAY KDYYVPMNKA LWKDLELKKI
     SKQELVNTRF SRLFSHFGQE KDGSFLAQRY QFYLAQQGQT LSGAHDLLDS LIERDYDLYA
     ATNGITAIQT GRLAQSGLVP YFNQVFISEQ LQTQKPDALF YEKIGQQIAG FSKEKTLMIG
     DSLTADIQGG NNAGIDTIWY NPHHLENHTQ AQPTYEVYSY QDLLDCLDKN ILEKITF
//