P0A6M4 (DTD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
D-tyrosyl-tRNA(Tyr) deacylase
EC=3.1.-.-

Gene names

Name:	dtd
Synonyms:	yihZ
Ordered Locus Names:	b3887, JW3858

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	145 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine. Can also cleave D-aspartyl-tRNA(Asp) and D-tryptophanyl-tRNA(Trp). HAMAP-Rule MF_00518
Subunit structure	Homodimer.
Subcellular location	Cytoplasm Probable HAMAP-Rule MF_00518.
Sequence similarities	Belongs to the DTD family.

Ontologies

Keywords
Cellular component	Cytoplasm
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	D-amino acid catabolic process Inferred from electronic annotation. Source: HAMAP tRNA metabolic process Inferred from mutant phenotype Ref.4. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	D-tyrosyl-tRNA(Tyr) deacylase activity Inferred from direct assay Ref.4. Source: EcoCyc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
cca	P06961	1	EBI-562575,EBI-545256

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 145

145

D-tyrosyl-tRNA(Tyr) deacylase HAMAP-Rule MF_00518

PRO_0000164537

Sites

Active site

80

1

Nucleophile By similarity

Secondary structure

1

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145

Helix Strand Turn

Details...

Beta strand

2 – 15

14

Beta strand

18 – 32

15

Helix

39 – 51

13

Beta strand

62 – 64

3

Turn

66 – 70

5

Beta strand

72 – 77

6

Helix

79 – 82

4

Beta strand

86 – 90

5

Beta strand

94 – 96

3

Helix

99 – 115

17

Beta strand

120 – 122

3

Beta strand

129 – 144

16

Sequences

	Sequence		Length	Mass (Da)
	P0A6M4 [UniParc]. Last modified May 10, 2005. Version 1. Checksum: 5CF0C0DB0819EC9B	FASTA	145	15,950
	10 20 30 40 50 60 MIALIQRVTR ASVTVEGEVT GEIGAGLLVL LGVEKDDDEQ KANRLCERVL GYRIFSDAEG 70 80 90 100 110 120 KMNLNVQQAG GSVLVVSQFT LAADTERGMR PSFSKGASPD RAEALYDYFV ERCRQQEMNT 130 140 QTGRFAADMQ VSLVNDGPVT FWLQV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes." Plunkett G. III, Burland V., Daniels D.L., Blattner F.R. Nucleic Acids Res. 21:3391-3398(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[2]	"The complete genome sequence of Escherichia coli K-12." 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. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Functional characterization of the D-Tyr-tRNATyr deacylase from Escherichia coli." Soutourina J., Plateau P., Delort F., Peirotes A., Blanquet S. J. Biol. Chem. 274:19109-19114(1999) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION, PROTEIN SEQUENCE OF 1-10. Strain: K12 / K37.
[5]	"Metabolism of D-aminoacyl-tRNAs in Escherichia coli and Saccharomyces cerevisiae cells." Soutourina J., Plateau P., Blanquet S. J. Biol. Chem. 275:32535-32542(2000) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION. Strain: K12 / K37.
[6]	"Structure of crystalline D-Tyr-tRNA(Tyr) deacylase. A representative of a new class of tRNA-dependent hydrolases." Ferri-Fioni M.-L., Schmitt E., Soutourina J., Plateau P., Mechulam Y., Blanquet S. J. Biol. Chem. 276:47285-47290(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS). Strain: K12 / K37.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L19201 Genomic DNA. Translation: AAB03020.1.
U00096 Genomic DNA. Translation: AAD13449.1.
AP009048 Genomic DNA. Translation: BAE77422.1.

PIR

S40831.

RefSeq

NP_418323.1. NC_000913.2.
YP_491563.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1JKE	X-ray	1.55	A/B/C/D	1-145	[»]

ProteinModelPortal

P0A6M4.

SMR

P0A6M4. Positions 1-145.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-47962N.

IntAct

P0A6M4. 9 interactions.

STRING

511145.b3887.

Proteomic databases

PaxDb

P0A6M4.

PRIDE

P0A6M4.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAD13449; AAD13449; b3887.
BAE77422; BAE77422; BAE77422.

GeneID

12933646.
948378.

KEGG

ecj:Y75_p3299.
eco:b3887.

PATRIC

32123277. VBIEscCol129921_3999.

Organism-specific databases

EchoBASE

EB1798.

EcoGene

EG11852. dtd.

Phylogenomic databases

eggNOG

COG1490.

HOGENOM

HOG000113982.

KO

K07560.

OMA

DGPVTIW.

ProtClustDB

PRK05273.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11852-MONOMER.
ECOL316407:JW3858-MONOMER.

Gene expression databases

Genevestigator

P0A6M4.

Family and domain databases

Gene3D

3.50.80.10. 1 hit.

HAMAP

MF_00518. Tyr_Deacylase_Dtd.

InterPro

IPR023509. DTD-like_dom.
IPR003732. DTyrtRNA_deacyls.
[Graphical view]

PANTHER

PTHR10472. PTHR10472. 1 hit.

Pfam

PF02580. Tyr_Deacylase. 1 hit.
[Graphical view]

SUPFAM

SSF69500. DTyrtRNA_deacyls. 1 hit.

TIGRFAMs

TIGR00256. TIGR00256. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P0A6M4.

Entry information

Entry name

DTD_ECOLI

Accession

Primary (citable) accession number: P0A6M4
Secondary accession number(s): P32147, Q2M8I4

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2005
Last sequence update:	May 10, 2005
Last modified:	May 1, 2013
This is version 73 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program