TRUD_ECOLI
ID TRUD_ECOLI Reviewed; 349 AA.
AC Q57261; Q2MA84;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 164.
DE RecName: Full=tRNA pseudouridine synthase D;
DE EC=5.4.99.27;
DE AltName: Full=tRNA pseudouridine(13) synthase;
DE AltName: Full=tRNA pseudouridylate synthase D;
DE AltName: Full=tRNA-uridine isomerase D;
GN Name=truD; Synonyms=ygbO; OrderedLocusNames=b2745, JW2715;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=MP180;
RX PubMed=7928962; DOI=10.1128/jb.176.19.6015-6022.1994;
RA Li C., Ichikawa J.K., Ravetto J.J., Kuo H.-C., Fu J.C., Clarke S.;
RT "A new gene involved in stationary-phase survival located at 59 minutes on
RT the Escherichia coli chromosome.";
RL J. Bacteriol. 176:6015-6022(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP PROTEIN SEQUENCE OF 1-10, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE
RP SPECIFICITY, AND MUTAGENESIS OF ASP-80.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=12756329; DOI=10.1261/rna.5230603;
RA Kaya Y., Ofengand J.;
RT "A novel unanticipated type of pseudouridine synthase with homologs in
RT bacteria, archaea, and eukarya.";
RL RNA 9:711-721(2003).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=B / BL21;
RX PubMed=10493123;
RX DOI=10.1002/(sici)1522-2683(19990801)20:11<2181::aid-elps2181>3.0.co;2-q;
RA Fountoulakis M., Takacs M.-F., Berndt P., Langen H., Takacs B.;
RT "Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite
RT chromatography.";
RL Electrophoresis 20:2181-2195(1999).
RN [6]
RP CRYSTALLIZATION, AND SUBUNIT.
RC STRAIN=K12;
RX PubMed=15039583; DOI=10.1107/s0907444904003506;
RA Ericsson U.B., Andersson M.E., Engvall B., Nordlund P., Hallberg B.M.;
RT "Expression, purification, crystallization and preliminary diffraction
RT studies of the tRNA pseudouridine synthase TruD from Escherichia coli.";
RL Acta Crystallogr. D 60:775-776(2004).
RN [7]
RP CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-31; LYS-79; GLN-87; ASN-129 AND
RP PHE-131, PROPOSED REACTION MECHANISM, AND ACTIVE SITE.
RX PubMed=19664587; DOI=10.1016/j.abb.2009.07.023;
RA Chan C.M., Huang R.H.;
RT "Enzymatic characterization and mutational studies of TruD--the fifth
RT family of pseudouridine synthases.";
RL Arch. Biochem. Biophys. 489:15-19(2009).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
RX PubMed=15135053; DOI=10.1016/j.febslet.2004.03.085;
RA Ericsson U.B., Nordlund P., Hallberg B.M.;
RT "X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted
RT domain with a novel fold.";
RL FEBS Lett. 565:59-64(2004).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
RX PubMed=14999002; DOI=10.1074/jbc.c400072200;
RA Kaya Y., Del Campo M., Ofengand J., Malhotra A.;
RT "Crystal structure of TruD, a novel pseudouridine synthase with a new
RT protein fold.";
RL J. Biol. Chem. 279:18107-18110(2004).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
RX PubMed=15208439; DOI=10.1261/rna.7240504;
RA Hoang C., Ferre-D'Amare A.R.;
RT "Crystal structure of the highly divergent pseudouridine synthase TruD
RT reveals a circular permutation of a conserved fold.";
RL RNA 10:1026-1033(2004).
CC -!- FUNCTION: Responsible for synthesis of pseudouridine from uracil-13 in
CC transfer RNAs. {ECO:0000269|PubMed:12756329}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=uridine(13) in tRNA = pseudouridine(13) in tRNA;
CC Xref=Rhea:RHEA:42540, Rhea:RHEA-COMP:10105, Rhea:RHEA-COMP:10106,
CC ChEBI:CHEBI:65314, ChEBI:CHEBI:65315; EC=5.4.99.27;
CC Evidence={ECO:0000269|PubMed:12756329, ECO:0000269|PubMed:19664587};
CC -!- SUBUNIT: Monomer. {ECO:0000305|PubMed:15039583}.
CC -!- SIMILARITY: Belongs to the pseudouridine synthase TruD family.
CC {ECO:0000305}.
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DR EMBL; L07942; AAA79838.1; -; Genomic_DNA.
DR EMBL; U29579; AAA69255.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75787.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76822.1; -; Genomic_DNA.
DR PIR; I69731; I69731.
DR RefSeq; NP_417225.1; NC_000913.3.
DR RefSeq; WP_000568943.1; NZ_STEB01000027.1.
DR PDB; 1SB7; X-ray; 2.20 A; A/B=1-349.
DR PDB; 1SI7; X-ray; 2.20 A; A=1-349.
DR PDB; 1SZW; X-ray; 2.00 A; A/B=1-349.
DR PDBsum; 1SB7; -.
DR PDBsum; 1SI7; -.
DR PDBsum; 1SZW; -.
DR AlphaFoldDB; Q57261; -.
DR SMR; Q57261; -.
DR BioGRID; 4262278; 41.
DR BioGRID; 851546; 2.
DR IntAct; Q57261; 9.
DR STRING; 511145.b2745; -.
DR jPOST; Q57261; -.
DR PaxDb; Q57261; -.
DR PRIDE; Q57261; -.
DR EnsemblBacteria; AAC75787; AAC75787; b2745.
DR EnsemblBacteria; BAE76822; BAE76822; BAE76822.
DR GeneID; 66673381; -.
DR GeneID; 947214; -.
DR KEGG; ecj:JW2715; -.
DR KEGG; eco:b2745; -.
DR PATRIC; fig|1411691.4.peg.3995; -.
DR EchoBASE; EB2912; -.
DR eggNOG; COG0585; Bacteria.
DR HOGENOM; CLU_005281_4_0_6; -.
DR InParanoid; Q57261; -.
DR OMA; LWLWVEK; -.
DR PhylomeDB; Q57261; -.
DR BioCyc; EcoCyc:G7422-MON; -.
DR BioCyc; MetaCyc:G7422-MON; -.
DR BRENDA; 5.4.99.27; 2026.
DR EvolutionaryTrace; Q57261; -.
DR PRO; PR:Q57261; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0009982; F:pseudouridine synthase activity; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0106029; F:tRNA pseudouridine synthase activity; IDA:EcoCyc.
DR GO; GO:0001522; P:pseudouridine synthesis; IDA:EcoCyc.
DR GO; GO:0031119; P:tRNA pseudouridine synthesis; IMP:EcoCyc.
DR Gene3D; 3.30.2340.10; -; 1.
DR Gene3D; 3.30.2350.20; -; 1.
DR HAMAP; MF_01082; TruD; 1.
DR InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR InterPro; IPR001656; PsdUridine_synth_TruD.
DR InterPro; IPR020119; PsdUridine_synth_TruD_CS.
DR InterPro; IPR011760; PsdUridine_synth_TruD_insert.
DR InterPro; IPR042214; TruD_catalytic.
DR InterPro; IPR043165; TruD_insert_sf.
DR Pfam; PF01142; TruD; 2.
DR SUPFAM; SSF55120; SSF55120; 1.
DR TIGRFAMs; TIGR00094; tRNA_TruD_broad; 1.
DR PROSITE; PS50984; TRUD; 1.
DR PROSITE; PS01268; UPF0024; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Isomerase; Reference proteome;
KW tRNA processing.
FT CHAIN 1..349
FT /note="tRNA pseudouridine synthase D"
FT /id="PRO_0000152495"
FT DOMAIN 155..303
FT /note="TRUD"
FT REGION 180..187
FT /note="RNA binding"
FT /evidence="ECO:0000305"
FT ACT_SITE 31
FT /note="Proton acceptor"
FT /evidence="ECO:0000255"
FT ACT_SITE 80
FT /note="Nucleophile"
FT /evidence="ECO:0000269|PubMed:19664587"
FT BINDING 27
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 129
FT /ligand="substrate"
FT /evidence="ECO:0000305"
FT BINDING 329
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MUTAGEN 31
FT /note="E->D: 3-fold decrease in activity."
FT /evidence="ECO:0000269|PubMed:19664587"
FT MUTAGEN 31
FT /note="E->Q: Loss of activity."
FT /evidence="ECO:0000269|PubMed:19664587"
FT MUTAGEN 79
FT /note="K->L: 20-fold decrease in activity."
FT /evidence="ECO:0000269|PubMed:19664587"
FT MUTAGEN 79
FT /note="K->R: 10-fold decrease in activity."
FT /evidence="ECO:0000269|PubMed:19664587"
FT MUTAGEN 80
FT /note="D->N,T: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12756329"
FT MUTAGEN 87
FT /note="Q->E: 3-fold decrease in activity."
FT /evidence="ECO:0000269|PubMed:19664587"
FT MUTAGEN 129
FT /note="N->K: Loss of activity."
FT /evidence="ECO:0000269|PubMed:19664587"
FT MUTAGEN 131
FT /note="F->Y: 1.5-fold decrease in activity."
FT /evidence="ECO:0000269|PubMed:19664587"
FT HELIX 4..6
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 15..17
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 19..23
FT /evidence="ECO:0007829|PDB:1SZW"
FT HELIX 24..26
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 27..32
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 41..53
FT /evidence="ECO:0007829|PDB:1SZW"
FT HELIX 55..65
FT /evidence="ECO:0007829|PDB:1SZW"
FT HELIX 70..72
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 73..76
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 83..92
FT /evidence="ECO:0007829|PDB:1SZW"
FT HELIX 101..103
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 109..119
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 128..137
FT /evidence="ECO:0007829|PDB:1SZW"
FT HELIX 141..154
FT /evidence="ECO:0007829|PDB:1SZW"
FT HELIX 162..165
FT /evidence="ECO:0007829|PDB:1SZW"
FT HELIX 167..169
FT /evidence="ECO:0007829|PDB:1SZW"
FT HELIX 170..179
FT /evidence="ECO:0007829|PDB:1SZW"
FT HELIX 189..210
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 213..215
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 224..227
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 233..235
FT /evidence="ECO:0007829|PDB:1SZW"
FT HELIX 238..240
FT /evidence="ECO:0007829|PDB:1SZW"
FT HELIX 241..249
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 252..259
FT /evidence="ECO:0007829|PDB:1SZW"
FT HELIX 269..278
FT /evidence="ECO:0007829|PDB:1SZW"
FT TURN 279..281
FT /evidence="ECO:0007829|PDB:1SZW"
FT HELIX 283..291
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 297..303
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 306..314
FT /evidence="ECO:0007829|PDB:1SZW"
FT STRAND 317..325
FT /evidence="ECO:0007829|PDB:1SZW"
FT HELIX 330..334
FT /evidence="ECO:0007829|PDB:1SZW"
FT TURN 335..337
FT /evidence="ECO:0007829|PDB:1SZW"
SQ SEQUENCE 349 AA; 39091 MW; 45282BA3F2CCD64B CRC64;
MIEFDNLTYL HGKPQGTGLL KANPEDFVVV EDLGFEPDGE GEHILVRILK NGCNTRFVAD
ALAKFLKIHA REVSFAGQKD KHAVTEQWLC ARVPGKEMPD LSAFQLEGCQ VLEYARHKRK
LRLGALKGNA FTLVLREVSN RDDVEQRLID ICVKGVPNYF GAQRFGIGGS NLQGAQRWAQ
TNTPVRDRNK RSFWLSAARS ALFNQIVAER LKKADVNQVV DGDALQLAGR GSWFVATTEE
LAELQRRVND KELMITAALP GSGEWGTQRE ALAFEQAAVA AETELQALLV REKVEAARRA
MLLYPQQLSW NWWDDVTVEI RFWLPAGSFA TSVVRELINT TGDYAHIAE
