PYNA_STRR6
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 03-AUG-2022, entry version 101.
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 AlphaFoldDB; Q8DPQ3; -.
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 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:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0106411; F:XMP 5'-nucleosidase activity; IEA:UniProtKB-EC.
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/PynA.
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 BINDING 9
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P95649"
FT BINDING 11
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P95649"
FT BINDING 181
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
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
