DTDA_PYRHO
ID DTDA_PYRHO Reviewed; 274 AA.
AC O57774;
DT 06-JUN-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 25-MAY-2022, entry version 117.
DE RecName: Full=D-aminoacyl-tRNA deacylase {ECO:0000255|HAMAP-Rule:MF_00562};
DE EC=3.1.1.96 {ECO:0000255|HAMAP-Rule:MF_00562};
DE AltName: Full=D-tyrosyl-tRNA(Tyr) deacylase;
GN Name=dtdA {ECO:0000255|HAMAP-Rule:MF_00562}; OrderedLocusNames=PH0006;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS).
RG Midwest center for structural genomics (MCSG);
RT "Structure of hypothetical protein ph0006 from Pyrococcus horikoshii.";
RL Submitted (APR-2006) to the PDB data bank.
CC -!- FUNCTION: D-aminoacyl-tRNA deacylase with broad substrate specificity.
CC By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules,
CC this enzyme counteracts the toxicity associated with the formation of
CC D-aminoacyl-tRNA entities in vivo. {ECO:0000255|HAMAP-Rule:MF_00562}.
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_00562};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala);
CC Xref=Rhea:RHEA:53744, Rhea:RHEA-COMP:9657, Rhea:RHEA-COMP:13640,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:57305,
CC ChEBI:CHEBI:78442, ChEBI:CHEBI:78522; EC=3.1.1.96;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00562};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00562};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_00562};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00562}.
CC -!- SIMILARITY: Belongs to the DtdA deacylase family. {ECO:0000255|HAMAP-
CC Rule:MF_00562}.
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DR EMBL; BA000001; BAA29074.1; -; Genomic_DNA.
DR PIR; C71218; C71218.
DR RefSeq; WP_010884126.1; NC_000961.1.
DR PDB; 2GFQ; X-ray; 1.75 A; A/B/C=1-274.
DR PDBsum; 2GFQ; -.
DR AlphaFoldDB; O57774; -.
DR SMR; O57774; -.
DR STRING; 70601.3256391; -.
DR EnsemblBacteria; BAA29074; BAA29074; BAA29074.
DR GeneID; 1443908; -.
DR KEGG; pho:PH0006; -.
DR eggNOG; arCOG01616; Archaea.
DR OMA; CYEATHH; -.
DR OrthoDB; 84039at2157; -.
DR EvolutionaryTrace; O57774; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0051499; F:D-aminoacyl-tRNA deacylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0019478; P:D-amino acid catabolic process; IEA:UniProtKB-UniRule.
DR HAMAP; MF_00562; Deacylase_DtdA; 1.
DR InterPro; IPR018033; Deacylase_DtdA_archaea.
DR InterPro; IPR007508; DtdA.
DR PANTHER; PTHR34667; PTHR34667; 1.
DR Pfam; PF04414; tRNA_deacylase; 1.
DR PIRSF; PIRSF016210; UCP016210; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Zinc.
FT CHAIN 1..274
FT /note="D-aminoacyl-tRNA deacylase"
FT /id="PRO_0000158972"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:2GFQ"
FT HELIX 11..23
FT /evidence="ECO:0007829|PDB:2GFQ"
FT STRAND 27..33
FT /evidence="ECO:0007829|PDB:2GFQ"
FT STRAND 36..41
FT /evidence="ECO:0007829|PDB:2GFQ"
FT STRAND 44..51
FT /evidence="ECO:0007829|PDB:2GFQ"
FT HELIX 59..67
FT /evidence="ECO:0007829|PDB:2GFQ"
FT STRAND 72..81
FT /evidence="ECO:0007829|PDB:2GFQ"
FT STRAND 88..92
FT /evidence="ECO:0007829|PDB:2GFQ"
FT STRAND 95..98
FT /evidence="ECO:0007829|PDB:2GFQ"
FT STRAND 101..104
FT /evidence="ECO:0007829|PDB:2GFQ"
FT HELIX 114..127
FT /evidence="ECO:0007829|PDB:2GFQ"
FT STRAND 133..136
FT /evidence="ECO:0007829|PDB:2GFQ"
FT STRAND 148..158
FT /evidence="ECO:0007829|PDB:2GFQ"
FT HELIX 159..162
FT /evidence="ECO:0007829|PDB:2GFQ"
FT HELIX 165..185
FT /evidence="ECO:0007829|PDB:2GFQ"
FT TURN 186..188
FT /evidence="ECO:0007829|PDB:2GFQ"
FT STRAND 190..195
FT /evidence="ECO:0007829|PDB:2GFQ"
FT HELIX 202..210
FT /evidence="ECO:0007829|PDB:2GFQ"
FT STRAND 211..219
FT /evidence="ECO:0007829|PDB:2GFQ"
FT HELIX 221..223
FT /evidence="ECO:0007829|PDB:2GFQ"
FT HELIX 228..235
FT /evidence="ECO:0007829|PDB:2GFQ"
FT STRAND 238..240
FT /evidence="ECO:0007829|PDB:2GFQ"
FT STRAND 244..249
FT /evidence="ECO:0007829|PDB:2GFQ"
FT HELIX 254..267
FT /evidence="ECO:0007829|PDB:2GFQ"
FT STRAND 270..274
FT /evidence="ECO:0007829|PDB:2GFQ"
SQ SEQUENCE 274 AA; 30890 MW; 53BC968C224DCBB9 CRC64;
MKVIMTTKVD KASMNIMNKL IENFGFKETE YVFDGNPVYK RGDVLILTTN DEMIYYDYLD
REIENQLGFK PEIIAFASRH SSKQKLPALT THVTGNWGKA MYGGKDESFA VAIPSAMKLS
LLKMSELNDL GWTVCYEATH HGPTELEVPS FFIEIGSSEE EWINDRAGEI IAETIIYVLD
NYEKGRSKFK VALGIGGGHY APKQTKRALE GDLAFGHILP KYAQPVSRDV MIKALNRFGE
KVEAIYVDWK GSRGETRQLA KSLAQELGLE FIKD
