DTD3_SYNY3
ID DTD3_SYNY3 Reviewed; 261 AA.
AC P73335;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 118.
DE RecName: Full=D-aminoacyl-tRNA deacylase {ECO:0000255|HAMAP-Rule:MF_02048, ECO:0000305};
DE EC=3.1.1.96 {ECO:0000255|HAMAP-Rule:MF_02048, ECO:0000269|PubMed:19332551};
DE AltName: Full=D-tyrosyl-tRNA deacylase {ECO:0000303|PubMed:19332551};
GN Name=dtd3 {ECO:0000255|HAMAP-Rule:MF_02048, ECO:0000303|PubMed:19332551};
GN OrderedLocusNames=sll1786;
OS Synechocystis sp. (strain PCC 6803 / Kazusa).
OC Bacteria; Cyanobacteria; Synechococcales; Merismopediaceae; Synechocystis;
OC unclassified Synechocystis.
OX NCBI_TaxID=1111708;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=8905231; DOI=10.1093/dnares/3.3.109;
RA Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y.,
RA Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T.,
RA Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.,
RA Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence analysis of the genome of the unicellular cyanobacterium
RT Synechocystis sp. strain PCC6803. II. Sequence determination of the entire
RT genome and assignment of potential protein-coding regions.";
RL DNA Res. 3:109-136(1996).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND DISRUPTION PHENOTYPE.
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=19332551; DOI=10.1074/jbc.m808173200;
RA Wydau S., van der Rest G., Aubard C., Plateau P., Blanquet S.;
RT "Widespread distribution of cell defense against D-aminoacyl-tRNAs.";
RL J. Biol. Chem. 284:14096-14104(2009).
CC -!- FUNCTION: Catalyzes the hydrolysis of D-tyrosyl-tRNA(Tyr).
CC {ECO:0000255|HAMAP-Rule:MF_02048, ECO:0000269|PubMed:19332551}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA +
CC H(+); Xref=Rhea:RHEA:13953, Rhea:RHEA-COMP:10123, Rhea:RHEA-
CC COMP:10124, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:59871,
CC ChEBI:CHEBI:78442, ChEBI:CHEBI:79333; EC=3.1.1.96;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02048,
CC ECO:0000269|PubMed:19332551};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-tyrosyl-tRNA(Tyr) + H2O = D-tyrosine + tRNA(Tyr);
CC Xref=Rhea:RHEA:25347, Rhea:RHEA-COMP:9707, Rhea:RHEA-COMP:9872,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:58570, ChEBI:CHEBI:78442,
CC ChEBI:CHEBI:78723; Evidence={ECO:0000255|HAMAP-Rule:MF_02048,
CC ECO:0000269|PubMed:19332551};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:19332551};
CC -!- COFACTOR:
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:19332551};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:19332551};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:19332551};
CC Note=The enzyme activity depends on the nature of the second cofactor.
CC Enzyme containing simultaneously Zn(2+) and either Co(2+), Ni(2+) or
CC Mn(2+) exhibits high activity. Enzyme containing two Zn(2+) is poorly
CC active. {ECO:0000269|PubMed:19332551};
CC -!- ACTIVITY REGULATION: Negatively regulated by excess Zn(2+).
CC {ECO:0000269|PubMed:19332551}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.8 uM for D-tyrosyl-tRNA(Tyr) {ECO:0000269|PubMed:19332551};
CC Note=kcat is 7.5 sec(-1). {ECO:0000269|PubMed:19332551};
CC -!- DISRUPTION PHENOTYPE: Disruption of the gene increases sensitivity of
CC the cell to D-tyrosine. {ECO:0000269|PubMed:19332551}.
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC TatD-type hydrolase family. DTD3 subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_02048, ECO:0000305}.
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DR EMBL; BA000022; BAA17366.1; -; Genomic_DNA.
DR PIR; S77519; S77519.
DR AlphaFoldDB; P73335; -.
DR SMR; P73335; -.
DR STRING; 1148.1652444; -.
DR PaxDb; P73335; -.
DR EnsemblBacteria; BAA17366; BAA17366; BAA17366.
DR KEGG; syn:sll1786; -.
DR eggNOG; COG0084; Bacteria.
DR InParanoid; P73335; -.
DR OMA; PNEAPRI; -.
DR PhylomeDB; P73335; -.
DR BRENDA; 3.1.1.96; 382.
DR Proteomes; UP000001425; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0051499; F:D-aminoacyl-tRNA deacylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0004536; F:deoxyribonuclease activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019478; P:D-amino acid catabolic process; IEA:UniProtKB-UniRule.
DR CDD; cd01310; TatD_DNAse; 1.
DR HAMAP; MF_02048; Deacylase_DTD3; 1.
DR InterPro; IPR033665; Deacylase_DTD3.
DR InterPro; IPR018228; DNase_TatD-rel_CS.
DR InterPro; IPR015991; Hydrolase_TatD-type.
DR InterPro; IPR032466; Metal_Hydrolase.
DR InterPro; IPR001130; TatD-like.
DR Pfam; PF01026; TatD_DNase; 1.
DR PIRSF; PIRSF005902; DNase_TatD; 1.
DR SUPFAM; SSF51556; SSF51556; 1.
DR TIGRFAMs; TIGR00010; TIGR00010; 1.
DR PROSITE; PS01137; TATD_1; 1.
DR PROSITE; PS01091; TATD_3; 1.
PE 1: Evidence at protein level;
KW Cobalt; Hydrolase; Manganese; Metal-binding; Nickel; Reference proteome;
KW Zinc.
FT CHAIN 1..261
FT /note="D-aminoacyl-tRNA deacylase"
FT /id="PRO_0000202008"
FT BINDING 7
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02048"
FT BINDING 9
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02048"
FT BINDING 94
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02048"
FT BINDING 94
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02048"
FT BINDING 129
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02048"
FT BINDING 156
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02048"
FT BINDING 206
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02048"
SQ SEQUENCE 261 AA; 29258 MW; 7F897DF2FE5131A2 CRC64;
MHLVDTHVHI NFDVFAADLD QLQHRWRQAG VVQLVHSCVK PQEFDQIQSL ADRFPELFFA
VGLHPLDAED WQDNTAGQIL AYAKADDRVV AIGEMGLDFF KADNRDHQIE VFRAQLAIAR
ELNKPVIIHC RDAAQTMRQV LTDFQAESGP VAGVMHCWGG TPEETQWFLD LGFYISFSGT
VTFKKAEGIQ ASAQMVPPDR LLVETDCPFL APVPQRGKRN EPAFVRHVAE AIAALRHVPL
ETLAQQTTTN ARNLFKLPVP A
