ID DTD_BACSU Reviewed; 132 AA.
AC O32042;
DT 23-JAN-2002, integrated into UniProtKB/Swiss-Prot.
DT 27-SEP-2017, sequence version 3.
DT 27-MAR-2024, entry version 129.
DE RecName: Full=Inactive D-aminoacyl-tRNA deacylase;
GN Name=dtd {ECO:0000255|HAMAP-Rule:MF_00518}; Synonyms=yrvI;
GN OrderedLocusNames=BSU27590;
OS Bacillus subtilis (strain 168).
OC Bacteria; Bacillota; 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 LACK OF DTD ACTIVITY.
RC STRAIN=SB19;
RX PubMed=4292198; DOI=10.1016/0022-2836(67)90259-8;
RA Calendar R., Berg P.;
RT "D-tyrosyl RNA: formation, hydrolysis and utilization for protein
RT synthesis.";
RL J. Mol. Biol. 26:39-54(1967).
RN [3]
RP LACK OF DTD ACTIVITY, AND RESTORATION OF ACTIVITY.
RC STRAIN=168, and
RC 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 /
RC NRRL NRS-744 / VKM B-501;
RX PubMed=24097941; DOI=10.1128/jb.00975-13;
RA Leiman S.A., May J.M., Lebar M.D., Kahne D., Kolter R., Losick R.;
RT "D-amino acids indirectly inhibit biofilm formation in Bacillus subtilis by
RT interfering with protein synthesis.";
RL J. Bacteriol. 195:5391-5395(2013).
RN [4]
RP LACK OF DTD ACTIVITY, AND BIOTECHNOLOGY.
RC STRAIN=168;
RX PubMed=25441601; DOI=10.1016/j.micres.2014.11.001;
RA Geraskina N.V., Butov I.A., Yomantas Y.A., Stoynova N.V.;
RT "The dtd gene from Bacillus amyloliquefaciens encodes a putative D-tyrosyl-
RT tRNATyr deacylase and is a selectable marker for Bacillus subtilis.";
RL Microbiol. Res. 171:90-96(2015).
CC -!- FUNCTION: A non-functional D-aminoacyl-tRNA deacylase (PubMed:4292198,
CC PubMed:24097941, PubMed:25441601). {ECO:0000269|PubMed:24097941,
CC ECO:0000269|PubMed:25441601, ECO:0000305|PubMed:4292198}.
CC -!- BIOTECHNOLOGY: The dtd gene from B.amyloliquefaciens strain A50 confers
CC the ability to grow in the presence of 20 mg/ml D-Tyr and 500 mg/ml D-
CC Asp to B.subtilis, showing it can be used as a selective marker in
CC bacteria that do not have a functional copy of this gene. Spontaneous
CC resistance to D-Tyr is very rare, on the order of 10(-9)
CC (PubMed:25441601). {ECO:0000269|PubMed:25441601}.
CC -!- MISCELLANEOUS: Culture in the presence of D-Leu, D-Met, D-Trp or D-Tyr
CC leads to growth inhibition due to their incorporation into protein, as
CC well as inhibition of biofilm formation (PubMed:24097941). Partially
CC contradictory results are seen in another study where growth occurs in
CC the presence of 20 and 500 mg/ml D-Trp but not in 500 mg/ml D-Asp or D-
CC Ser; whether these are the exact same strains is unknown
CC (PubMed:25441601). Strains in which this gene is restored by
CC mutagenesis are resistant to D-Leu, D-Met, D-Trp and D-Tyr and form
CC biofilm even in the presence of D-amino acids, while maintaining the
CC ability to incorporate at least D-Trp into peptidoglycan
CC (PubMed:24097941). {ECO:0000269|PubMed:24097941,
CC ECO:0000269|PubMed:25441601}.
CC -!- SIMILARITY: Belongs to the DTD family. {ECO:0000255|HAMAP-
CC Rule:MF_00518}.
CC -!- CAUTION: Could be the product of a pseudogene. The lack of an
CC initiation codon prevents translation of this gene, in agreement with
CC the observation that D-Tyr-tRNA(Tyr) deacylase activity cannot be
CC detected in some strains of B.subtilis (PubMed:4292198,
CC PubMed:24097941, PubMed:25441601). Mutagenesis to restore the start
CC codon (in strain NCIB 3610, the parent of the fully sequenced 168)
CC confers resistance to D-Tyr (PubMed:24097941).
CC {ECO:0000269|PubMed:24097941, ECO:0000269|PubMed:25441601,
CC ECO:0000305|PubMed:4292198}.
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DR EMBL; AL009126; CAB14718.2; -; Genomic_DNA.
DR PIR; A69981; A69981.
DR RefSeq; NP_390637.2; NC_000964.3.
DR RefSeq; WP_003229749.1; NZ_CP051860.2.
DR AlphaFoldDB; O32042; -.
DR SMR; O32042; -.
DR STRING; 224308.BSU27590; -.
DR PaxDb; 224308-BSU27590; -.
DR EnsemblBacteria; CAB14718; CAB14718; BSU_27590.
DR GeneID; 936530; -.
DR KEGG; bsu:BSU27590; -.
DR PATRIC; fig|224308.43.peg.2880; -.
DR eggNOG; COG1490; Bacteria.
DR InParanoid; O32042; -.
DR OrthoDB; 9801395at2; -.
DR BioCyc; BSUB:BSU27590-MONOMER; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0051500; F:D-tyrosyl-tRNA(Tyr) deacylase activity; IBA:GO_Central.
DR GO; GO:0106026; F:Gly-tRNA(Ala) hydrolase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0043908; F:Ser(Gly)-tRNA(Ala) hydrolase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0019478; P:D-amino acid catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006399; P:tRNA metabolic process; IBA:GO_Central.
DR CDD; cd00563; Dtyr_deacylase; 1.
DR Gene3D; 3.50.80.10; D-tyrosyl-tRNA(Tyr) deacylase; 1.
DR HAMAP; MF_00518; Deacylase_Dtd; 1.
DR InterPro; IPR003732; Daa-tRNA_deacyls_DTD.
DR InterPro; IPR023509; DTD-like_sf.
DR NCBIfam; TIGR00256; D-aminoacyl-tRNA deacylase; 1.
DR PANTHER; PTHR10472:SF5; D-AMINOACYL-TRNA DEACYLASE 1; 1.
DR PANTHER; PTHR10472; D-TYROSYL-TRNA TYR DEACYLASE; 1.
DR Pfam; PF02580; Tyr_Deacylase; 1.
DR SUPFAM; SSF69500; DTD-like; 1.
PE 5: Uncertain;
KW Reference proteome.
FT CHAIN 1..132
FT /note="Inactive D-aminoacyl-tRNA deacylase"
FT /id="PRO_0000164625"
SQ SEQUENCE 132 AA; 14487 MW; 61DFB081591E6D7B CRC64;
MDEEVVGQIG QGLMVLVGIT HDDTEDDAAY LADKVVNLRI FDDSEGKMNL SLVDIGGEIL
SVSQFTLYGD TKKGRRPNYM NAAKPDKALG LYEKWNDLLR EKGIKVETGT FGAMMDVQLT
NSGPVTLIMD SK
//
