P07649 (TRUA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
tRNA pseudouridine synthase A
EC=5.4.99.12

Alternative name(s):
tRNA pseudouridine(38-40) synthase
tRNA pseudouridylate synthase I
Short name=PSU-I
tRNA-uridine isomerase I

Gene names

Name:	truA
Synonyms:	asuC, hisT, leuK
Ordered Locus Names:	b2318, JW2315

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	270 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs. Ref.11
Catalytic activity	tRNA uridine(38-40) = tRNA pseudouridine(38-40). Ref.11
Subunit structure	Homodimer. Ref.10 Ref.11
Sequence similarities	Belongs to the tRNA pseudouridine synthase TruA family.

Ontologies

Keywords
Biological process	tRNA processing
Molecular function	Isomerase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	tRNA pseudouridine synthesis Inferred from mutant phenotype PubMed 192717. Source: EcoCyc
Molecular_function	pseudouridine synthase activity Inferred from direct assay Ref.7. Source: EcoCyc tRNA binding Inferred from direct assay Ref.7. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 270

270

tRNA pseudouridine synthase A HAMAP-Rule MF_00171

PRO_0000057375

Regions

Region

107 – 111

5

RNA binding HAMAP-Rule MF_00171

Region

168 – 172

5

Interaction with tRNA HAMAP-Rule MF_00171

Sites

Active site

60

1

Nucleophile Ref.8 Ref.9

Binding site

118

1

Substrate

Site

58

1

Interaction with tRNA; Important for base-flipping

Site

78

1

Interaction with tRNA

Site

110

1

Interaction with tRNA

Site

126

1

Interaction with tRNA

Site

139

1

Interaction with tRNA

Experimental info

Mutagenesis

58

1

R → A: Loss of activity. Ref.11

Secondary structure

1

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270

Helix Strand Turn

Details...

Beta strand

10 – 18

9

Helix

20 – 22

3

Beta strand

30 – 32

3

Helix

35 – 47

13

Beta strand

53 – 57

5

Beta strand

64 – 75

12

Helix

80 – 89

10

Beta strand

95 – 102

8

Turn

109 – 112

4

Beta strand

115 – 123

9

Beta strand

125 – 127

3

Turn

131 – 134

4

Beta strand

135 – 138

4

Helix

145 – 152

8

Helix

153 – 155

3

Beta strand

157 – 160

4

Helix

162 – 164

3

Beta strand

175 – 186

12

Beta strand

189 – 197

9

Helix

203 – 215

13

Helix

223 – 230

8

Helix

233 – 235

3

Beta strand

245 – 251

7

Helix

254 – 256

3

Sequences

	Sequence		Length	Mass (Da)
	P07649 [UniParc]. Last modified April 1, 1988. Version 1. Checksum: 8E97BC88C3220188	FASTA	270	30,400
	10 20 30 40 50 60 MSDQQQPPVY KIALGIEYDG SKYYGWQRQN EVRSVQEKLE KALSQVANEP ITVFCAGRTD 70 80 90 100 110 120 AGVHGTGQVV HFETTALRKD AAWTLGVNAN LPGDIAVRWV KTVPDDFHAR FSATARRYRY 130 140 150 160 170 180 IIYNHRLRPA VLSKGVTHFY EPLDAERMHR AAQCLLGEND FTSFRAVQCQ SRTPWRNVMH 190 200 210 220 230 240 INVTRHGPYV VVDIKANAFV HHMVRNIVGS LMEVGAHNQP ESWIAELLAA KDRTLAAATA 250 260 270 KAEGLYLVAV DYPDRYDLPK PPMGPLFLAD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structural features of the hisT operon of Escherichia coli K-12." Arps P.J., Marvel C.C., Rubin B.C., Tolan D.A., Penhoet E.E., Winkler M.E. Nucleic Acids Res. 13:5297-5315(1985) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T. DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"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.
[4]	"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.
[5]	"The hisT-purF region of the Escherichia coli K-12 chromosome. Identification of additional genes of the hisT and purF operons." Nonet M.L., Marvel C.C., Tolan D.R. J. Biol. Chem. 262:12209-12217(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 255-270. Strain: K12.
[6]	"Structural analysis of the Escherichia coli K-12 hisT operon by using a kanamycin resistance cassette." Arps P.J., Winkler M.E. J. Bacteriol. 169:1061-1070(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-10 AND 267-270. Strain: K12.
[7]	"Purification, structure, and properties of Escherichia coli tRNA pseudouridine synthase I." Kammen H.O., Marvel C.C., Hardy L., Penhoet E.E. J. Biol. Chem. 263:2255-2263(1988) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE, CHARACTERIZATION.
[8]	"A conserved aspartate of tRNA pseudouridine synthase is essential for activity and a probable nucleophilic catalyst." Huang L., Pookanjanatavip M., Gu X., Santi D.V. Biochemistry 37:344-351(1998) [PubMed] [Europe PMC] [Abstract] Cited for: ACTIVE SITE.
[9]	"The mechanism of pseudouridine synthase I as deduced from its interaction with 5-fluorouracil-tRNA." Gu X., Liu Y., Santi D.V. Proc. Natl. Acad. Sci. U.S.A. 96:14270-14275(1999) [PubMed] [Europe PMC] [Abstract] Cited for: ACTIVE SITE.
[10]	"The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I." Foster P.G., Huang L., Santi D.V., Stroud R.M. Nat. Struct. Biol. 7:23-27(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 7-270, SUBUNIT.
[11]	"How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA." Hur S., Stroud R.M. Mol. Cell 26:189-203(2007) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.9 ANGSTROMS) OF 7-270 IN COMPLEX WITH TRNA, CATALYTIC ACTIVITY, FUNCTION, SUBUNIT, MUTAGENESIS OF ARG-58.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X02743 Genomic DNA. Translation: CAA26522.1.
U00096 Genomic DNA. Translation: AAC75378.1.
AP009048 Genomic DNA. Translation: BAA16175.1.
M68934 Genomic DNA. Translation: AAA23963.1.
M15542 Genomic DNA. Translation: AAA24313.1.
M15543 Genomic DNA. No translation available.

PIR

SYECZ1. B23792.

RefSeq

NP_416821.1. NC_000913.2.
YP_490560.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DJ0	X-ray	1.50	A/B	7-270	[»]
2NQP	X-ray	3.50	A/B/C/D	7-270	[»]
2NR0	X-ray	3.90	A/B/C/D	7-270	[»]
2NRE	X-ray	4.00	A	7-270	[»]

ProteinModelPortal

P07649.

SMR

P07649. Positions 7-270.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-11043N.

IntAct

P07649. 4 interactions.

MINT

MINT-1310146.

STRING

511145.b2318.

Proteomic databases

PaxDb

P07649.

PRIDE

P07649.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75378; AAC75378; b2318.
BAA16175; BAA16175; BAA16175.

GeneID

12932365.
946793.

KEGG

ecj:Y75_p2284.
eco:b2318.

PATRIC

32120007. VBIEscCol129921_2413.

Organism-specific databases

EchoBASE

EB0449.

EcoGene

EG10454. truA.

Phylogenomic databases

eggNOG

COG0101.

HOGENOM

HOG000248672.

KO

K06173.

OMA

TPFRNVH.

ProtClustDB

PRK00021.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10454-MONOMER.
ECOL316407:JW2315-MONOMER.
MetaCyc:EG10454-MONOMER.

BRENDA

5.4.99.12. 2026.

Gene expression databases

Genevestigator

P07649.

Family and domain databases

Gene3D

3.30.70.580. 1 hit.
3.30.70.660. 1 hit.

HAMAP

MF_00171. TruA.

InterPro

IPR020103. PsdUridine_synth_cat_dom.
IPR001406. PsdUridine_synth_TruA.
IPR020097. PsdUridine_synth_TruA_a/b_dom.
IPR020095. PsdUridine_synth_TruA_C.
IPR020094. PsdUridine_synth_TruA_N.
[Graphical view]

PANTHER

PTHR11142. PTHR11142. 1 hit.

Pfam

PF01416. PseudoU_synth_1. 2 hits.
[Graphical view]

PIRSF

PIRSF001430. tRNA_psdUrid_synth. 1 hit.

SUPFAM

SSF55120. PsdUridine_synth_cat_dom. 1 hit.

TIGRFAMs

TIGR00071. hisT_truA. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P07649.

Entry information

Entry name

TRUA_ECOLI

Accession

Primary (citable) accession number: P07649

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	April 1, 1988
Last modified:	May 1, 2013
This is version 127 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program