5DNU_ECOLI
ID 5DNU_ECOLI Reviewed; 199 AA.
AC P76491; Q2MAM2;
DT 27-MAR-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 160.
DE RecName: Full=5'-deoxynucleotidase YfbR {ECO:0000255|HAMAP-Rule:MF_01100};
DE EC=3.1.3.89 {ECO:0000255|HAMAP-Rule:MF_01100, ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:18353368};
DE AltName: Full=5'-deoxyribonucleotidase {ECO:0000255|HAMAP-Rule:MF_01100, ECO:0000303|PubMed:18353368};
DE AltName: Full=Nucleoside 5'-monophosphate phosphohydrolase {ECO:0000255|HAMAP-Rule:MF_01100};
GN Name=yfbR {ECO:0000255|HAMAP-Rule:MF_01100};
GN OrderedLocusNames=b2291, JW2288;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR, SUBUNIT,
RP ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=15489502; DOI=10.1074/jbc.m411023200;
RA Proudfoot M., Kuznetsova E., Brown G., Rao N.N., Kitagawa M., Mori H.,
RA Savchenko A., Yakunin A.F.;
RT "General enzymatic screens identify three new nucleotidases in Escherichia
RT coli. Biochemical characterization of SurE, YfbR, and YjjG.";
RL J. Biol. Chem. 279:54687-54694(2004).
RN [4]
RP FUNCTION IN THE SYNTHESIS OF THYMIDYLATE.
RX PubMed=17827303; DOI=10.1128/jb.00461-07;
RA Weiss B.;
RT "The deoxycytidine pathway for thymidylate synthesis in Escherichia coli.";
RL J. Bacteriol. 189:7922-7926(2007).
RN [5] {ECO:0007744|PDB:2PAQ, ECO:0007744|PDB:2PAR, ECO:0007744|PDB:2PAU}
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF MUTANT ALA-72 IN COMPLEX WITH
RP COBALT ION AND SUBSTRATES, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND MUTAGENESIS OF ARG-18; VAL-30;
RP HIS-33; HIS-68; ASP-69; GLU-72; ASP-77; GLU-122 AND ASP-137.
RX PubMed=18353368; DOI=10.1016/j.jmb.2008.02.036;
RA Zimmerman M.D., Proudfoot M., Yakunin A., Minor W.;
RT "Structural insight into the mechanism of substrate specificity and
RT catalytic activity of an HD-domain phosphohydrolase: the 5'-
RT deoxyribonucleotidase YfbR from Escherichia coli.";
RL J. Mol. Biol. 378:215-226(2008).
CC -!- FUNCTION: Essential component of the deoxycytidine triphosphate (dCTP)
CC pathway for de novo synthesis of thymidylate. Catalyzes the strictly
CC specific dephosphorylation of 2'-deoxyribonucleoside 5'-monophosphates
CC (dAMP, dGMP, dTMP, dUMP, dIMP and dCMP) and does not dephosphorylate
CC 5'-ribonucleotides or ribonucleoside 3'-monophosphates.
CC {ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:17827303,
CC ECO:0000269|PubMed:18353368}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-phosphate + H2O = a 2'-
CC deoxyribonucleoside + phosphate; Xref=Rhea:RHEA:36167,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:18274, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:65317; EC=3.1.3.89; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01100, ECO:0000269|PubMed:15489502,
CC ECO:0000269|PubMed:18353368};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dAMP + H2O = 2'-deoxyadenosine + phosphate;
CC Xref=Rhea:RHEA:29371, ChEBI:CHEBI:15377, ChEBI:CHEBI:17256,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:58245;
CC Evidence={ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:18353368};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dGMP + H2O = 2'-deoxyguanosine + phosphate;
CC Xref=Rhea:RHEA:29379, ChEBI:CHEBI:15377, ChEBI:CHEBI:17172,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57673;
CC Evidence={ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:18353368};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dTMP + H2O = phosphate + thymidine; Xref=Rhea:RHEA:11080,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:17748, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:63528; Evidence={ECO:0000269|PubMed:15489502,
CC ECO:0000269|PubMed:18353368};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dUMP + H2O = 2'-deoxyuridine + phosphate;
CC Xref=Rhea:RHEA:29355, ChEBI:CHEBI:15377, ChEBI:CHEBI:16450,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:246422;
CC Evidence={ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:18353368};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dIMP + H2O = 2'-deoxyinosine + phosphate;
CC Xref=Rhea:RHEA:29383, ChEBI:CHEBI:15377, ChEBI:CHEBI:28997,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:61194;
CC Evidence={ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:18353368};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dCMP + H2O = 2'-deoxycytidine + phosphate;
CC Xref=Rhea:RHEA:29363, ChEBI:CHEBI:15377, ChEBI:CHEBI:15698,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57566;
CC Evidence={ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:18353368};
CC -!- COFACTOR:
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:18353368};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:15489502};
CC Name=Cu(2+); Xref=ChEBI:CHEBI:29036;
CC Evidence={ECO:0000269|PubMed:15489502};
CC Note=A divalent metal cation. Highest activity with Co(2+), followed by
CC Mn(2+) and Cu(2+). {ECO:0000269|PubMed:15489502};
CC -!- ACTIVITY REGULATION: Inhibited by both ribo- and deoxyribonucleoside
CC di- and triphosphates. {ECO:0000269|PubMed:15489502}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.012 mM for 5'-dAMP {ECO:0000269|PubMed:15489502};
CC KM=0.017 mM for 5'-dAMP {ECO:0000269|PubMed:18353368};
CC KM=0.047 mM for 5'-dGMP {ECO:0000269|PubMed:15489502};
CC KM=0.008 mM for 5'-dTMP {ECO:0000269|PubMed:15489502};
CC KM=0.020 mM for 5'-dUMP {ECO:0000269|PubMed:15489502};
CC KM=0.017 mM for 5'-dIMP {ECO:0000269|PubMed:15489502};
CC KM=0.036 mM for 5'-dCMP {ECO:0000269|PubMed:15489502};
CC KM=2.09 mM for pNPP {ECO:0000269|PubMed:15489502};
CC Vmax=0.71 umol/min/mg enzyme with 5'-dAMP as substrate
CC {ECO:0000269|PubMed:15489502};
CC Vmax=0.36 umol/min/mg enzyme with 5'-dAMP as substrate
CC {ECO:0000269|PubMed:18353368};
CC Vmax=0.46 umol/min/mg enzyme with 5'-dGMP as substrate
CC {ECO:0000269|PubMed:15489502};
CC Vmax=0.37 umol/min/mg enzyme with 5'-dTMP as substrate
CC {ECO:0000269|PubMed:15489502};
CC Vmax=0.54 umol/min/mg enzyme with 5'-dUMP as substrate
CC {ECO:0000269|PubMed:15489502};
CC Vmax=0.56 umol/min/mg enzyme with 5'-dIMP as substrate
CC {ECO:0000269|PubMed:15489502};
CC Vmax=0.53 umol/min/mg enzyme with 5'-dCMP as substrate
CC {ECO:0000269|PubMed:15489502};
CC Vmax=1.32 umol/min/mg enzyme with pNPP as substrate
CC {ECO:0000269|PubMed:15489502};
CC pH dependence:
CC Optimum pH is 8.0. {ECO:0000269|PubMed:15489502};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01100,
CC ECO:0000269|PubMed:15489502, ECO:0000269|PubMed:18353368}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01100,
CC ECO:0000305}.
CC -!- SIMILARITY: Belongs to the 5DNU family. {ECO:0000255|HAMAP-
CC Rule:MF_01100, ECO:0000305}.
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DR EMBL; U00096; AAC75351.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76684.1; -; Genomic_DNA.
DR PIR; A65001; A65001.
DR RefSeq; NP_416794.1; NC_000913.3.
DR RefSeq; WP_000813859.1; NZ_LN832404.1.
DR PDB; 2PAQ; X-ray; 2.10 A; A/B=1-199.
DR PDB; 2PAR; X-ray; 2.10 A; A/B=1-199.
DR PDB; 2PAU; X-ray; 2.10 A; A/B=1-199.
DR PDBsum; 2PAQ; -.
DR PDBsum; 2PAR; -.
DR PDBsum; 2PAU; -.
DR AlphaFoldDB; P76491; -.
DR SMR; P76491; -.
DR BioGRID; 4262969; 28.
DR DIP; DIP-28107N; -.
DR IntAct; P76491; 2.
DR STRING; 511145.b2291; -.
DR jPOST; P76491; -.
DR PaxDb; P76491; -.
DR PRIDE; P76491; -.
DR EnsemblBacteria; AAC75351; AAC75351; b2291.
DR EnsemblBacteria; BAE76684; BAE76684; BAE76684.
DR GeneID; 946771; -.
DR KEGG; ecj:JW2288; -.
DR KEGG; eco:b2291; -.
DR PATRIC; fig|1411691.4.peg.4444; -.
DR EchoBASE; EB3855; -.
DR eggNOG; COG1896; Bacteria.
DR HOGENOM; CLU_084784_0_0_6; -.
DR InParanoid; P76491; -.
DR OMA; NQSHFFA; -.
DR PhylomeDB; P76491; -.
DR BioCyc; EcoCyc:G7185-MON; -.
DR BioCyc; MetaCyc:G7185-MON; -.
DR BRENDA; 3.1.3.5; 2026.
DR BRENDA; 3.1.3.89; 2026.
DR SABIO-RK; P76491; -.
DR EvolutionaryTrace; P76491; -.
DR PRO; PR:P76491; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0002953; F:5'-deoxynucleotidase activity; IDA:EcoCyc.
DR GO; GO:0050897; F:cobalt ion binding; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0050340; F:thymidylate 5'-phosphatase activity; IEA:RHEA.
DR GO; GO:0006226; P:dUMP biosynthetic process; IMP:EcoCyc.
DR GO; GO:0010139; P:pyrimidine deoxyribonucleotide salvage; IMP:EcoCyc.
DR CDD; cd00077; HDc; 1.
DR HAMAP; MF_01100; 5DNU; 1.
DR InterPro; IPR003607; HD/PDEase_dom.
DR InterPro; IPR006674; HD_domain.
DR InterPro; IPR022971; YfbR.
DR InterPro; IPR039356; YfbR/HDDC2.
DR PANTHER; PTHR11845; PTHR11845; 1.
DR SMART; SM00471; HDc; 1.
DR PROSITE; PS51831; HD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalt; Copper; Cytoplasm; Hydrolase; Manganese;
KW Metal-binding; Nucleotide-binding; Reference proteome.
FT CHAIN 1..199
FT /note="5'-deoxynucleotidase YfbR"
FT /id="PRO_0000095049"
FT DOMAIN 30..142
FT /note="HD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01175"
FT BINDING 18..19
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18353368,
FT ECO:0007744|PDB:2PAU"
FT BINDING 33
FT /ligand="Co(2+)"
FT /ligand_id="ChEBI:CHEBI:48828"
FT /evidence="ECO:0000269|PubMed:18353368,
FT ECO:0007744|PDB:2PAR, ECO:0007744|PDB:2PAU"
FT BINDING 33
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18353368,
FT ECO:0007744|PDB:2PAU"
FT BINDING 68
FT /ligand="Co(2+)"
FT /ligand_id="ChEBI:CHEBI:48828"
FT /evidence="ECO:0000269|PubMed:18353368,
FT ECO:0007744|PDB:2PAR, ECO:0007744|PDB:2PAU"
FT BINDING 69
FT /ligand="Co(2+)"
FT /ligand_id="ChEBI:CHEBI:48828"
FT /evidence="ECO:0000269|PubMed:18353368,
FT ECO:0007744|PDB:2PAR, ECO:0007744|PDB:2PAU"
FT BINDING 69
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18353368"
FT BINDING 77..80
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18353368,
FT ECO:0007744|PDB:2PAU"
FT BINDING 137
FT /ligand="Co(2+)"
FT /ligand_id="ChEBI:CHEBI:48828"
FT /evidence="ECO:0000269|PubMed:18353368,
FT ECO:0007744|PDB:2PAR, ECO:0007744|PDB:2PAU"
FT BINDING 137
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:18353368,
FT ECO:0007744|PDB:2PAU"
FT SITE 18
FT /note="Appears to be important in orienting the phosphate
FT for catalysis"
FT MUTAGEN 18
FT /note="R->A: Shows negligible enzymatic activity."
FT /evidence="ECO:0000269|PubMed:18353368"
FT MUTAGEN 30
FT /note="V->A: Shows reduced activity and affinity compared
FT to the wild-type."
FT /evidence="ECO:0000269|PubMed:18353368"
FT MUTAGEN 33
FT /note="H->A: Shows negligible enzymatic activity."
FT /evidence="ECO:0000269|PubMed:18353368"
FT MUTAGEN 68
FT /note="H->A: Shows negligible enzymatic activity."
FT /evidence="ECO:0000269|PubMed:18353368"
FT MUTAGEN 69
FT /note="D->A: Shows negligible enzymatic activity."
FT /evidence="ECO:0000269|PubMed:18353368"
FT MUTAGEN 72
FT /note="E->A: Shows negligible enzymatic activity."
FT /evidence="ECO:0000269|PubMed:18353368"
FT MUTAGEN 72
FT /note="E->V: Shows wild-type activity and substrate
FT affinity."
FT /evidence="ECO:0000269|PubMed:18353368"
FT MUTAGEN 77
FT /note="D->A: Shows negligible enzymatic activity."
FT /evidence="ECO:0000269|PubMed:18353368"
FT MUTAGEN 122
FT /note="E->A: Shows reduced activity and affinity compared
FT to the wild-type."
FT /evidence="ECO:0000269|PubMed:18353368"
FT MUTAGEN 137
FT /note="D->A: Shows negligible enzymatic activity."
FT /evidence="ECO:0000269|PubMed:18353368"
FT HELIX 6..10
FT /evidence="ECO:0007829|PDB:2PAQ"
FT HELIX 11..15
FT /evidence="ECO:0007829|PDB:2PAQ"
FT HELIX 30..51
FT /evidence="ECO:0007829|PDB:2PAQ"
FT HELIX 58..67
FT /evidence="ECO:0007829|PDB:2PAQ"
FT TURN 68..71
FT /evidence="ECO:0007829|PDB:2PAQ"
FT HELIX 72..75
FT /evidence="ECO:0007829|PDB:2PAQ"
FT HELIX 93..105
FT /evidence="ECO:0007829|PDB:2PAQ"
FT HELIX 110..112
FT /evidence="ECO:0007829|PDB:2PAQ"
FT HELIX 113..120
FT /evidence="ECO:0007829|PDB:2PAQ"
FT TURN 121..123
FT /evidence="ECO:0007829|PDB:2PAQ"
FT HELIX 127..150
FT /evidence="ECO:0007829|PDB:2PAQ"
FT HELIX 154..156
FT /evidence="ECO:0007829|PDB:2PAQ"
FT HELIX 157..169
FT /evidence="ECO:0007829|PDB:2PAQ"
FT HELIX 173..182
FT /evidence="ECO:0007829|PDB:2PAQ"
FT HELIX 184..186
FT /evidence="ECO:0007829|PDB:2PAR"
SQ SEQUENCE 199 AA; 22708 MW; 895E9A06130DA057 CRC64;
MKQSHFFAHL SRLKLINRWP LMRNVRTENV SEHSLQVAMV AHALAAIKNR KFGGNVNAER
IALLAMYHDA SEVLTGDLPT PVKYFNSQIA QEYKAIEKIA QQKLVDMVPE ELRDIFAPLI
DEHAYSDEEK SLVKQADALC AYLKCLEELA AGNNEFLLAK TRLEATLEAR RSQEMDYFME
IFVPSFHLSL DEISQDSPL
