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

 DTD_PLAF7               Reviewed;         164 AA.
Q8IIS0;
27-SEP-2017, integrated into UniProtKB/Swiss-Prot.
01-MAR-2003, sequence version 1.
23-MAY-2018, entry version 112.
RecName: Full=D-aminoacyl-tRNA deacylase;
Short=DTD {ECO:0000303|PubMed:20445234};
EC=3.1.1.96 {ECO:0000269|PubMed:24302572, ECO:0000305|PubMed:20007323};
AltName: Full=D-Tyrosyl-tRNA(Tyr) deacylase {ECO:0000303|PubMed:20445234};
AltName: Full=Gly-tRNA(Ala) deacylase {ECO:0000303|PubMed:28362257};
EC=3.1.1.- {ECO:0000269|PubMed:28362257};
AltName: Full=Gly-tRNA(Gly) deacylase {ECO:0000303|PubMed:27224426};
Name=dtd {ECO:0000303|PubMed:20007323};
ORFNames=PF11_0095, PF3D7_1108200;
Plasmodium falciparum (isolate 3D7).
Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida;
Plasmodiidae; Plasmodium; Plasmodium (Laverania).
NCBI_TaxID=36329;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Isolate 3D7;
PubMed=12368864; DOI=10.1038/nature01097;
Gardner M.J., Hall N., Fung E., White O., Berriman M., Hyman R.W.,
Carlton J.M., Pain A., Nelson K.E., Bowman S., Paulsen I.T.,
James K.D., Eisen J.A., Rutherford K.M., Salzberg S.L., Craig A.,
Kyes S., Chan M.-S., Nene V., Shallom S.J., Suh B., Peterson J.,
Angiuoli S., Pertea M., Allen J., Selengut J., Haft D., Mather M.W.,
Vaidya A.B., Martin D.M.A., Fairlamb A.H., Fraunholz M.J., Roos D.S.,
Ralph S.A., McFadden G.I., Cummings L.M., Subramanian G.M.,
Mungall C., Venter J.C., Carucci D.J., Hoffman S.L., Newbold C.,
Davis R.W., Fraser C.M., Barrell B.G.;
"Genome sequence of the human malaria parasite Plasmodium
falciparum.";
Nature 419:498-511(2002).
[2]
FUNCTION, AND CATALYTIC ACTIVITY.
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).
[3] {ECO:0000244|PDB:3LMT, ECO:0000244|PDB:3LMU, ECO:0000244|PDB:3LMV}
X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS).
PubMed=20445234; DOI=10.1107/S0907444910006062;
Yogavel M., Khan S., Bhatt T.K., Sharma A.;
"Structure of D-tyrosyl-tRNATyr deacylase using home-source Cu Kalpha
and moderate-quality iodide-SAD data: structural polymorphism and
HEPES-bound enzyme states.";
Acta Crystallogr. D 66:584-592(2010).
[4] {ECO:0000244|PDB:3KNF, ECO:0000244|PDB:3KNP, ECO:0000244|PDB:3KO3, ECO:0000244|PDB:3KO4, ECO:0000244|PDB:3KO5, ECO:0000244|PDB:3KO7, ECO:0000244|PDB:3KO9, ECO:0000244|PDB:3KOB, ECO:0000244|PDB:3KOC, ECO:0000244|PDB:3KOD}
X-RAY CRYSTALLOGRAPHY (2.09 ANGSTROMS) IN COMPLEX WITH D-AMINO ACIDS,
FUNCTION, CATALYTIC ACTIVITY, POSSIBLE REACTION MECHANISM, SUBUNIT,
AND SUBCELLULAR LOCATION.
PubMed=20007323; DOI=10.1074/jbc.M109.038562;
Bhatt T.K., Yogavel M., Wydau S., Berwal R., Sharma A.;
"Ligand-bound structures provide atomic snapshots for the catalytic
mechanism of D-amino acid deacylase.";
J. Biol. Chem. 285:5917-5930(2010).
[5] {ECO:0000244|PDB:4NBI, ECO:0000244|PDB:4NBJ}
X-RAY CRYSTALLOGRAPHY (1.86 ANGSTROMS) IN COMPLEX WITH SUBSTRATE
ANALOG, FUNCTION, POSSIBLE REACTION MECHANISM, SUBUNIT, DOMAIN, AND
MUTAGENESIS OF SER-87; GLN-88; THR-90; ALA-112; PHE-137; GLY-149 AND
PRO-150.
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).
[6] {ECO:0000244|PDB:5J61}
X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH GLY SUBSTRATE
ANALOG, FUNCTION, SUBSTRATE SPECIFICITY, AND MUTAGENESIS OF ALA-112
AND PHE-137.
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).
-!- FUNCTION: D-aminoacyl-tRNA deacylase, with no observable activity
on tRNAs charged with their cognate L-amino acid (PubMed:20007323,
PubMed:24302572, PubMed:27224426). Probably acts by rejecting L-
amino acids from its binding site rather than specific recognition
of D-amino acids (PubMed:27224426). Catalyzes the hydrolysis of D-
tyrosyl-tRNA(Tyr), has no activity on correctly charged L-tyrosyl-
tRNA(Tyr) (PubMed:20007323, PubMed:24302572, PubMed:27224426).
Hydrolyzes correctly charged, achiral, glycyl-tRNA(Gly)
(PubMed:27224426). Deacylates mischarged D.melanogaster and E.coli
glycyl-tRNA(Ala) (PubMed:28362257). Probably acts via tRNA-based
rather than protein-based catalysis (PubMed:24302572,
PubMed:27224426). Acts on tRNAs only when the D-amino acid is
either attached to the ribose 3'-OH or transferred to the 3'-OH
from the 2'-OH through rapid transesterification
(PubMed:24302572). Binds a number of other D-amino acids (D-Arg,
D-Glu, D-His, D-Lys, D-Ser), suggesting it may also deacylate
other mischarged tRNAs (PubMed:20007323).
{ECO:0000269|PubMed:20007323, ECO:0000269|PubMed:24302572,
ECO:0000269|PubMed:27224426, ECO:0000269|PubMed:28362257}.
-!- CATALYTIC ACTIVITY: Glycyl-tRNA(Ala) + H(2)O = glycine +
tRNA(Ala). {ECO:0000269|PubMed:28362257}.
-!- CATALYTIC ACTIVITY: A D-aminoacyl-tRNA + H(2)O = a D-amino acid +
tRNA. {ECO:0000269|PubMed:24302572, ECO:0000305|PubMed:20007323}.
-!- SUBUNIT: Homodimer (PubMed:20007323, PubMed:24302572).
{ECO:0000269|PubMed:20007323, ECO:0000269|PubMed:24302572}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:20007323}.
-!- 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:0000269|PubMed:24302572, ECO:0000269|PubMed:27224426}.
-!- MISCELLANEOUS: In the crystal structures with bound ADP (PDB 3KO4,
3KO5), the adenosine moiety is thought to represent the authentic
C-terminal adenosine of charged tRNA and is annotated as such in
this entry (PubMed:20007323). {ECO:0000305|PubMed:20007323}.
-!- SIMILARITY: Belongs to the DTD family.
-!- CAUTION: Initially the conserved reside Thr-90 was thought to be a
nucleophile; mutagenesis in this organism and E.coli indicates it
is not. {ECO:0000269|PubMed:24302572}.
-----------------------------------------------------------------------
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EMBL; AE014186; AAN35683.1; -; Genomic_DNA.
EMBL; LN999945; CZT98748.1; -; Genomic_DNA.
RefSeq; XP_001347770.1; XM_001347734.1.
PDB; 3KNF; X-ray; 3.00 A; A/B/C/D/E/F=1-164.
PDB; 3KNP; X-ray; 3.30 A; A/B/C/D/E/F=1-164.
PDB; 3KO3; X-ray; 2.80 A; A/B/C/D/E/F=1-164.
PDB; 3KO4; X-ray; 2.70 A; A/B/C/D/E/F=1-164.
PDB; 3KO5; X-ray; 2.09 A; A/B/C/D/E/F=1-164.
PDB; 3KO7; X-ray; 2.21 A; A/B/C/D/E/F=1-164.
PDB; 3KO9; X-ray; 2.75 A; A/B/C/D/E/F=1-164.
PDB; 3KOB; X-ray; 2.99 A; A/B/C/D/E/F=1-164.
PDB; 3KOC; X-ray; 2.91 A; A/B/C/D/E/F=1-164.
PDB; 3KOD; X-ray; 3.00 A; A/B/C/D/E/F=1-164.
PDB; 3LMT; X-ray; 2.75 A; A/B/C/D/E/F=1-164.
PDB; 3LMU; X-ray; 3.30 A; A/B/C/D/E/F/G/H=1-164.
PDB; 3LMV; X-ray; 2.83 A; A/B/C/D/E/F=1-164.
PDB; 4NBI; X-ray; 1.86 A; A/B=1-164.
PDB; 4NBJ; X-ray; 2.20 A; A/B/C/D/E/F/G/H=1-164.
PDB; 5J61; X-ray; 2.10 A; A/B/C/D/E/F/G/H=1-164.
PDBsum; 3KNF; -.
PDBsum; 3KNP; -.
PDBsum; 3KO3; -.
PDBsum; 3KO4; -.
PDBsum; 3KO5; -.
PDBsum; 3KO7; -.
PDBsum; 3KO9; -.
PDBsum; 3KOB; -.
PDBsum; 3KOC; -.
PDBsum; 3KOD; -.
PDBsum; 3LMT; -.
PDBsum; 3LMU; -.
PDBsum; 3LMV; -.
PDBsum; 4NBI; -.
PDBsum; 4NBJ; -.
PDBsum; 5J61; -.
SMR; Q8IIS0; -.
PRIDE; Q8IIS0; -.
EnsemblProtists; CZT98748; CZT98748; PF3D7_1108200.
GeneDB; PF3D7_1108200.1:pep; -.
GeneID; 810646; -.
KEGG; pfa:PF11_0095; -.
EuPathDB; PlasmoDB:PF3D7_1108200; -.
HOGENOM; HOG000113981; -.
InParanoid; Q8IIS0; -.
KO; K07560; -.
OMA; GVFQAHM; -.
EvolutionaryTrace; Q8IIS0; -.
Proteomes; UP000001450; Chromosome 11.
GO; GO:0005737; C:cytoplasm; IDA:GeneDB.
GO; GO:0002161; F:aminoacyl-tRNA editing activity; IBA:GO_Central.
GO; GO:0051500; F:D-tyrosyl-tRNA(Tyr) deacylase activity; IDA:UniProtKB.
GO; GO:0106026; F:Gly-tRNA(Ala) hydrolase activity; IDA:UniProtKB.
GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
GO; GO:0006399; P:tRNA metabolic process; IBA:GO_Central.
Gene3D; 3.50.80.10; -; 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; Hydrolase;
Nucleotide-binding; Reference proteome; RNA-binding; tRNA-binding.
CHAIN 1 164 D-aminoacyl-tRNA deacylase.
/FTId=PRO_0000441703.
MOTIF 104 107 C-terminal adenosine nucleotide of tRNA.
{ECO:0000244|PDB:3KO4,
ECO:0000244|PDB:3KO5,
ECO:0000305|PubMed:20007323}.
MOTIF 149 150 Gly-cisPro motif, allows the protein to
recognize chirality of D-amino acids.
{ECO:0000269|PubMed:24302572}.
ACT_SITE 90 90 Nucleophile.
{ECO:0000305|PubMed:20007323}.
BINDING 72 72 C-terminal adenosine nucleotide of tRNA.
{ECO:0000244|PDB:3KO5,
ECO:0000305|PubMed:20007323}.
BINDING 89 89 C-terminal adenosine nucleotide of tRNA.
{ECO:0000244|PDB:3KO4,
ECO:0000244|PDB:3KO5,
ECO:0000305|PubMed:20007323}.
MUTAGEN 87 87 S->A: Partial loss of deacylation of D-
tyrosyl-tRNA(Tyr).
{ECO:0000269|PubMed:24302572}.
MUTAGEN 87 87 S->P: Wild-type deacylation of D-tyrosyl-
tRNA(Tyr). {ECO:0000269|PubMed:24302572}.
MUTAGEN 88 88 Q->A,E,N: Wild-type deacylation of D-
tyrosyl-tRNA(Tyr).
{ECO:0000269|PubMed:24302572}.
MUTAGEN 90 90 T->A,S: Wild-type deacylation of D-
tyrosyl-tRNA(Tyr).
{ECO:0000269|PubMed:24302572}.
MUTAGEN 112 112 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 137 137 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 149 149 G->A: Loss of deacylation of D-tyrosyl-
tRNA(Tyr). {ECO:0000269|PubMed:24302572}.
MUTAGEN 150 150 P->A: Loss of deacylation of D-tyrosyl-
tRNA(Tyr). {ECO:0000269|PubMed:24302572}.
STRAND 2 16 {ECO:0000244|PDB:4NBI}.
STRAND 22 24 {ECO:0000244|PDB:3KO9}.
STRAND 27 42 {ECO:0000244|PDB:4NBI}.
HELIX 49 61 {ECO:0000244|PDB:4NBI}.
STRAND 65 67 {ECO:0000244|PDB:3KO5}.
STRAND 70 74 {ECO:0000244|PDB:3KO5}.
TURN 76 80 {ECO:0000244|PDB:4NBI}.
STRAND 82 87 {ECO:0000244|PDB:4NBI}.
HELIX 89 92 {ECO:0000244|PDB:4NBI}.
STRAND 96 100 {ECO:0000244|PDB:4NBI}.
STRAND 104 106 {ECO:0000244|PDB:3KO4}.
HELIX 109 126 {ECO:0000244|PDB:4NBI}.
HELIX 129 131 {ECO:0000244|PDB:4NBI}.
STRAND 132 134 {ECO:0000244|PDB:4NBI}.
STRAND 137 139 {ECO:0000244|PDB:3KOC}.
STRAND 141 156 {ECO:0000244|PDB:4NBI}.
HELIX 157 159 {ECO:0000244|PDB:4NBI}.
SEQUENCE 164 AA; 19205 MW; 305B8DA0CFC2508D CRC64;
MRVVIQRVKG AILSVRKENI GENEKELEII SEIKNGLICF LGIHKNDTWE DALYIIRKCL
NLRLWNNDNK TWDKNVKDLN YELLIVSQFT LFGNTKKGNK PDFHLAKEPN EALIFYNKII
DEFKKQYNDD KIKIGKFGNY MNIDVTNDGP VTIYIDTHDI NLNK


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