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D-aminoacyl-tRNA deacylase (DTD) (EC 3.1.1.96) (D-tyrosyl RNA deacylase) (D-tyrosyl-tRNA(Tyr) deacylase) (Gly-tRNA(Ala) deacylase) (EC 3.1.1.-) (Gly-tRNA(Gly) deacylase)

 DTD_ECOLI               Reviewed;         145 AA.
P0A6M4; P32147; Q2M8I4;
10-MAY-2005, integrated into UniProtKB/Swiss-Prot.
10-MAY-2005, sequence version 1.
28-MAR-2018, entry version 109.
RecName: Full=D-aminoacyl-tRNA deacylase {ECO:0000255|HAMAP-Rule:MF_00518, ECO:0000303|PubMed:10918062};
Short=DTD {ECO:0000255|HAMAP-Rule:MF_00518};
EC=3.1.1.96 {ECO:0000255|HAMAP-Rule:MF_00518, ECO:0000269|PubMed:10383414, ECO:0000269|PubMed:10918062, ECO:0000269|PubMed:4292198};
AltName: Full=D-tyrosyl RNA deacylase {ECO:0000303|PubMed:4292198};
AltName: Full=D-tyrosyl-tRNA(Tyr) deacylase {ECO:0000303|PubMed:10383414};
AltName: Full=Gly-tRNA(Ala) deacylase {ECO:0000255|HAMAP-Rule:MF_00518, ECO:0000303|PubMed:28362257};
EC=3.1.1.- {ECO:0000255|HAMAP-Rule:MF_00518, ECO:0000269|PubMed:28362257};
AltName: Full=Gly-tRNA(Gly) deacylase {ECO:0000303|PubMed:27224426};
Name=dtd {ECO:0000255|HAMAP-Rule:MF_00518,
ECO:0000303|PubMed:10918062}; Synonyms=yihZ;
OrderedLocusNames=b3887, JW3858;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=8346018; DOI=10.1093/nar/21.15.3391;
Plunkett G. III, Burland V., Daniels D.L., Blattner F.R.;
"Analysis of the Escherichia coli genome. III. DNA sequence of the
region from 87.2 to 89.2 minutes.";
Nucleic Acids Res. 21:3391-3398(1993).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[4]
PROTEIN SEQUENCE OF 1-10, FUNCTION, CATALYTIC ACTIVITY,
BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND DISRUPTION PHENOTYPE.
STRAIN=K12 / EC989, and K12 / K37;
PubMed=10383414; DOI=10.1074/jbc.274.27.19109;
Soutourina J., Plateau P., Delort F., Peirotes A., Blanquet S.;
"Functional characterization of the D-Tyr-tRNATyr deacylase from
Escherichia coli.";
J. Biol. Chem. 274:19109-19114(1999).
[5]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND SUBCELLULAR
LOCATION.
STRAIN=B;
PubMed=4292198; DOI=10.1016/0022-2836(67)90259-8;
Calendar R., Berg P.;
"D-tyrosyl RNA: formation, hydrolysis and utilization for protein
synthesis.";
J. Mol. Biol. 26:39-54(1967).
[6]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND DISRUPTION
PHENOTYPE.
STRAIN=K12 / K37;
PubMed=10918062; DOI=10.1074/jbc.M005166200;
Soutourina J., Plateau P., Blanquet S.;
"Metabolism of D-aminoacyl-tRNAs in Escherichia coli and Saccharomyces
cerevisiae cells.";
J. Biol. Chem. 275:32535-32542(2000).
[7]
FUNCTION, AND DISRUPTION PHENOTYPE.
STRAIN=K12 / K37;
PubMed=15292242; DOI=10.1074/jbc.M402931200;
Soutourina O., Soutourina J., Blanquet S., Plateau P.;
"Formation of D-tyrosyl-tRNATyr accounts for the toxicity of D-
tyrosine toward Escherichia coli.";
J. Biol. Chem. 279:42560-42565(2004).
[8]
FUNCTION, AND MUTAGENESIS OF MET-129.
PubMed=16902403; DOI=10.1038/sj.emboj.7601278;
Hussain T., Kruparani S.P., Pal B., Dock-Bregeon A.C., Dwivedi S.,
Shekar M.R., Sureshbabu K., Sankaranarayanan R.;
"Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like
domain in threonyl-tRNA synthetase from archaea.";
EMBO J. 25:4152-4162(2006).
[9]
FUNCTION, REACTION MECHANISM, DOMAIN, AND MUTAGENESIS OF SER-77;
GLN-78; THR-80; ALA-102; PHE-125; GLY-137 AND PRO-138.
PubMed=24302572; DOI=10.7554/eLife.01519;
Ahmad S., Routh S.B., Kamarthapu V., Chalissery J., Muthukumar S.,
Hussain T., Kruparani S.P., Deshmukh M.V., Sankaranarayanan R.;
"Mechanism of chiral proofreading during translation of the genetic
code.";
Elife 2:E01519-E01519(2013).
[10]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=25441601; DOI=10.1016/j.micres.2014.11.001;
Geraskina N.V., Butov I.A., Yomantas Y.A., Stoynova N.V.;
"The dtd gene from Bacillus amyloliquefaciens encodes a putative D-
tyrosyl-tRNATyr deacylase and is a selectable marker for Bacillus
subtilis.";
Microbiol. Res. 171:90-96(2015).
[11]
FUNCTION, SUBSTRATE SPECIFICITY, REACTION MECHANISM,
BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF ALA-102 AND PHE-125.
STRAIN=K12;
PubMed=27224426; DOI=10.1371/journal.pbio.1002465;
Routh S.B., Pawar K.I., Ahmad S., Singh S., Suma K., Kumar M.,
Kuncha S.K., Yadav K., Kruparani S.P., Sankaranarayanan R.;
"Elongation factor Tu prevents misediting of Gly-tRNA(Gly) caused by
the design behind the chiral proofreading site of D-aminoacyl-tRNA
deacylase.";
PLoS Biol. 14:E1002465-E1002465(2016).
[12]
FUNCTION, REACTION MECHANISM, CATALYTIC ACTIVITY, AND DISRUPTION
PHENOTYPE.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=28362257; DOI=10.7554/eLife.24001;
Pawar K.I., Suma K., Seenivasan A., Kuncha S.K., Routh S.B.,
Kruparani S.P., Sankaranarayanan R.;
"Role of D-aminoacyl-tRNA deacylase beyond chiral proofreading as a
cellular defense against glycine mischarging by AlaRS.";
Elife 6:0-0(2017).
[13] {ECO:0000244|PDB:1JKE}
X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS), AND SUBUNIT.
STRAIN=K12 / K37;
PubMed=11568181; DOI=10.1074/jbc.M106550200;
Ferri-Fioni M.-L., Schmitt E., Soutourina J., Plateau P., Mechulam Y.,
Blanquet S.;
"Structure of crystalline D-Tyr-tRNA(Tyr) deacylase. A representative
of a new class of tRNA-dependent hydrolases.";
J. Biol. Chem. 276:47285-47290(2001).
-!- FUNCTION: An aminoacyl-tRNA editing enzyme that deacylates
mischarged D-aminoacyl-tRNAs, has no observable editing activity
on tRNAs charged with cognate L-amino acid (PubMed:10383414,
PubMed:4292198, PubMed:10918062, PubMed:24302572,
PubMed:27224426). Edits mischarged glycyl-tRNA(Ala) more
efficiently than AlaRS (PubMed:28362257). Acts via tRNA-based
rather than protein-based catalysis (PubMed:24302572,
PubMed:27224426, PubMed:28362257). Rejects correctly charged L-
amino acid-tRNAs from its binding site rather than specifically
recognizing incorrectly charged D-amino acid-tRNAs
(PubMed:27224426). Hydrolyzes correctly charged, achiral, glycyl-
tRNA(Gly); GTP-bound EF-Tu (tested with T.thermophilus EF-Tu AC
Q5SHN6) protects charged glycyl-tRNA(Gly) from hydrolysis, while
increasing Dtd levels or inactivating EF-Tu decreases protection
(PubMed:27224426). Hydrolyzes mischarged glycyl-tRNA(Ala) (but not
seryl-tRNA(Ala)) even in the presence of EF-Tu, edits about 4-fold
better than the editing domain of AlaRS (PubMed:28362257). Has
greater activity on glycyl-tRNA(Ala) than glycyl-tRNA(Gly) due in
part to its recognition of the conserved tRNA(Ala) G3.U70 wobble
base pair (PubMed:28362257). Binds D-amino acids but not L-amino
acids (PubMed:16902403). Overexpression of E.coli or P.falciparum
Dtd is toxic in E.coli, toxicity can be rescued by supplementation
with Gly (PubMed:27224426). By recycling D-aminoacyl-tRNA to D-
amino acids and free tRNA molecules, this enzyme counteracts the
toxicity associated with the formation of D-aminoacyl-tRNA
entities in vivo and helps enforce protein L-homochirality
(PubMed:15292242). Hydrolyzes D-tyrosyl-tRNA(Tyr) (PubMed:4292198,
PubMed:10383414, PubMed:24302572, PubMed:27224426). Hydrolyzes D-
phenylalanyl-tRNA(Phe) (PubMed:4292198, PubMed:24302572).
Hydrolyzes D-aspartyl-tRNA(Asp) (PubMed:10918062). Hydrolyzes D-
tryptophanyl-tRNA(Trp) (PubMed:10918062). Hydrolyzes glycyl-
tRNA(Gly) (PubMed:27224426). Hydrolyzes glycyl-tRNA(Ala)
(PubMed:28362257). {ECO:0000269|PubMed:10383414,
ECO:0000269|PubMed:10918062, ECO:0000269|PubMed:15292242,
ECO:0000269|PubMed:16902403, ECO:0000269|PubMed:24302572,
ECO:0000269|PubMed:25441601, ECO:0000269|PubMed:27224426,
ECO:0000269|PubMed:28362257, ECO:0000269|PubMed:4292198}.
-!- CATALYTIC ACTIVITY: Glycyl-tRNA(Ala) + H(2)O = glycine +
tRNA(Ala). {ECO:0000255|HAMAP-Rule:MF_00518,
ECO:0000269|PubMed:28362257}.
-!- CATALYTIC ACTIVITY: A D-aminoacyl-tRNA + H(2)O = a D-amino acid +
tRNA. {ECO:0000255|HAMAP-Rule:MF_00518,
ECO:0000269|PubMed:10383414, ECO:0000269|PubMed:10918062,
ECO:0000269|PubMed:4292198}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=1.0 uM for D-tyrosyl-tRNA(Tyr) {ECO:0000269|PubMed:10383414};
KM=1.0 uM for glycyl-tRNA(Gly) {ECO:0000269|PubMed:27224426};
Note=kcat/KM is 6 uM(-1)s(-1) for D-tyrosyl-tRNA(Tyr)
(PubMed:10383414). kcat/KM is 2.8 uM(-1)s(-1) for D-
tryptophanyl-tRNA(Trp) (PubMed:10918062). kcat/KM is 12 uM(-
1)s(-1) for D-aspartyl-tRNA(Asp) (PubMed:10918062). kcat/KM is
10 uM (-1)s(-1) for glycyl-tRNA(Gly) (PubMed:27224426).
{ECO:0000269|PubMed:10383414, ECO:0000269|PubMed:10918062,
ECO:0000269|PubMed:27224426};
-!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00518,
ECO:0000269|PubMed:10383414, ECO:0000269|PubMed:11568181}.
-!- INTERACTION:
P06961:cca; NbExp=2; IntAct=EBI-562575, EBI-545256;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00518,
ECO:0000305|PubMed:4292198}.
-!- DOMAIN: A Gly-cisPro motif from one monomer fits into the active
site of the other monomer to allow specific chiral rejection of L-
amino acids (PubMed:24302572, PubMed:27224426).
{ECO:0000255|HAMAP-Rule:MF_00518, ECO:0000269|PubMed:24302572,
ECO:0000269|PubMed:27224426}.
-!- DISRUPTION PHENOTYPE: No phenotype in rich or minimal medium,
decreased growth rate in the presence of excess D-tyrosine
(PubMed:10383414). A double dtd-dadA deletion mutant has a more
pronounced growth defect in the presence of D-Tyr (in strain K12 /
EC989) (PubMed:10383414). In a dtd deletion mutant about 40% of
tRNA(Tyr) is D-tyrosyl-tRNA(Tyr); overexpressing the gene for
tRNA(Tyr) suppresses the toxicity of D-Tyr by increasing the
levels of L-tyrosyl-tRNA(Tyr) available for translation
(PubMed:15292242). Decreased growth in the presence of D-Asp, D-
Ser, D-Gln and D-Trp (PubMed:10918062). Poor growth on 20 mg/ml D-
Tyr, no growth on 500 mg/ml D-Tyr or 20 mg/ml D-Trp
(PubMed:25441601). Overexpression of genes for tRNA(Asp) or
tRNA(Trp) suppresses the toxicity of their respective D-amino
acids (PubMed:15292242). No effect seen when grown in 3 or 10 mM
Gly; in a mutant that no longer edits mischarged glycyl-tRNA(Ala)
or seryl-tRNA(Ala) (triple mutation in alaS) Gly becomes toxic,
but excess Ala restores growth (PubMed:28362257).
{ECO:0000269|PubMed:10383414, ECO:0000269|PubMed:10918062,
ECO:0000269|PubMed:15292242, ECO:0000269|PubMed:25441601,
ECO:0000269|PubMed:28362257}.
-!- SIMILARITY: Belongs to the DTD family. {ECO:0000255|HAMAP-
Rule:MF_00518}.
-!- CAUTION: Initially the conserved reside Thr-80 was thought to be a
nucleophile; mutagenesis in this organism and P.falciparum
indicates it is not. {ECO:0000269|PubMed:24302572}.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; L19201; AAB03020.1; -; Genomic_DNA.
EMBL; U00096; AAD13449.1; -; Genomic_DNA.
EMBL; AP009048; BAE77422.1; -; Genomic_DNA.
PIR; S40831; S40831.
RefSeq; NP_418323.1; NC_000913.3.
RefSeq; WP_000560983.1; NZ_LN832404.1.
PDB; 1JKE; X-ray; 1.55 A; A/B/C/D=1-145.
PDBsum; 1JKE; -.
ProteinModelPortal; P0A6M4; -.
SMR; P0A6M4; -.
BioGrid; 4262640; 2.
DIP; DIP-47962N; -.
IntAct; P0A6M4; 9.
STRING; 316385.ECDH10B_4077; -.
PaxDb; P0A6M4; -.
PRIDE; P0A6M4; -.
EnsemblBacteria; AAD13449; AAD13449; b3887.
EnsemblBacteria; BAE77422; BAE77422; BAE77422.
GeneID; 948378; -.
KEGG; ecj:JW3858; -.
KEGG; eco:b3887; -.
PATRIC; fig|1411691.4.peg.2824; -.
EchoBASE; EB1798; -.
EcoGene; EG11852; dtd.
eggNOG; ENOG4108YYA; Bacteria.
eggNOG; COG1490; LUCA.
HOGENOM; HOG000113982; -.
InParanoid; P0A6M4; -.
KO; K07560; -.
OMA; GVFQAHM; -.
PhylomeDB; P0A6M4; -.
BioCyc; EcoCyc:EG11852-MONOMER; -.
BioCyc; MetaCyc:EG11852-MONOMER; -.
BRENDA; 3.1.1.96; 2026.
EvolutionaryTrace; P0A6M4; -.
PRO; PR:P0A6M4; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
GO; GO:0002161; F:aminoacyl-tRNA editing activity; IDA:EcoCyc.
GO; GO:0051500; F:D-tyrosyl-tRNA(Tyr) deacylase activity; IDA:EcoCyc.
GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
GO; GO:0009408; P:response to heat; IMP:EcoCyc.
GO; GO:0006399; P:tRNA metabolic process; IMP:EcoCyc.
CDD; cd00563; Dtyr_deacylase; 1.
Gene3D; 3.50.80.10; -; 1.
HAMAP; MF_00518; Deacylase_Dtd; 1.
InterPro; IPR003732; Daa-tRNA_deacyls_DTD.
InterPro; IPR023509; DTD-like_sf.
PANTHER; PTHR10472; PTHR10472; 1.
Pfam; PF02580; Tyr_Deacylase; 1.
SUPFAM; SSF69500; SSF69500; 1.
TIGRFAMs; TIGR00256; TIGR00256; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Direct protein sequencing;
Hydrolase; Reference proteome; RNA-binding; tRNA-binding.
CHAIN 1 145 D-aminoacyl-tRNA deacylase.
/FTId=PRO_0000164537.
MOTIF 137 138 Gly-cisPro motif, important for rejection
of L-amino acids. {ECO:0000255|HAMAP-
Rule:MF_00518,
ECO:0000269|PubMed:24302572}.
MUTAGEN 77 77 S->A,P: Wild-type deacylation of D-
tyrosyl-tRNA(Tyr).
{ECO:0000269|PubMed:24302572}.
MUTAGEN 78 78 Q->A: Wild-type deacylation of D-tyrosyl-
tRNA(Tyr). {ECO:0000269|PubMed:24302572}.
MUTAGEN 80 80 T->A: Wild-type deacylation of D-tyrosyl-
tRNA(Tyr). {ECO:0000269|PubMed:24302572}.
MUTAGEN 102 102 A->F: Loss of deacylation of D-tyrosyl-
tRNA(Tyr), loss of deacylation of glycyl-
tRNA(Gly), not toxic upon overexpression.
{ECO:0000269|PubMed:24302572,
ECO:0000269|PubMed:27224426}.
MUTAGEN 125 125 F->A: Loss of deacylation of D-tyrosyl-
tRNA(Tyr), loss of deacylation of glycyl-
tRNA(Gly). {ECO:0000269|PubMed:24302572,
ECO:0000269|PubMed:27224426}.
MUTAGEN 129 129 M->K: Alters stereospecificity, confers
binding of L-amino acids while slightly
decreasing binding of D-amino acids.
{ECO:0000269|PubMed:16902403}.
MUTAGEN 137 137 G->A: Loss of deacylation of D-tyrosyl-
tRNA(Tyr). {ECO:0000269|PubMed:24302572}.
MUTAGEN 138 138 P->A: Loss of deacylation of D-tyrosyl-
tRNA(Tyr). {ECO:0000269|PubMed:24302572}.
STRAND 2 15 {ECO:0000244|PDB:1JKE}.
STRAND 18 32 {ECO:0000244|PDB:1JKE}.
HELIX 39 51 {ECO:0000244|PDB:1JKE}.
STRAND 62 64 {ECO:0000244|PDB:1JKE}.
TURN 66 70 {ECO:0000244|PDB:1JKE}.
STRAND 72 77 {ECO:0000244|PDB:1JKE}.
HELIX 79 82 {ECO:0000244|PDB:1JKE}.
STRAND 86 90 {ECO:0000244|PDB:1JKE}.
STRAND 94 96 {ECO:0000244|PDB:1JKE}.
HELIX 99 115 {ECO:0000244|PDB:1JKE}.
STRAND 120 122 {ECO:0000244|PDB:1JKE}.
STRAND 129 144 {ECO:0000244|PDB:1JKE}.
SEQUENCE 145 AA; 15950 MW; 5CF0C0DB0819EC9B CRC64;
MIALIQRVTR ASVTVEGEVT GEIGAGLLVL LGVEKDDDEQ KANRLCERVL GYRIFSDAEG
KMNLNVQQAG GSVLVVSQFT LAADTERGMR PSFSKGASPD RAEALYDYFV ERCRQQEMNT
QTGRFAADMQ VSLVNDGPVT FWLQV


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