TRUB_ECOLI
ID TRUB_ECOLI Reviewed; 314 AA.
AC P60340; P09171; P76671; Q2M944;
DT 16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT 16-FEB-2004, sequence version 1.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=tRNA pseudouridine synthase B {ECO:0000255|HAMAP-Rule:MF_01080};
DE EC=5.4.99.25 {ECO:0000255|HAMAP-Rule:MF_01080, ECO:0000269|PubMed:7489483};
DE AltName: Full=Protein P35 {ECO:0000303|PubMed:2849753};
DE AltName: Full=tRNA pseudouridine(55) synthase {ECO:0000255|HAMAP-Rule:MF_01080};
DE Short=Psi55 synthase {ECO:0000255|HAMAP-Rule:MF_01080};
DE AltName: Full=tRNA pseudouridylate synthase {ECO:0000255|HAMAP-Rule:MF_01080};
DE AltName: Full=tRNA-uridine isomerase {ECO:0000255|HAMAP-Rule:MF_01080};
GN Name=truB; Synonyms=yhbA; OrderedLocusNames=b3166, JW3135;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], INDUCTION, AND OPERON.
RC STRAIN=K12;
RX PubMed=2849753; DOI=10.1093/nar/16.22.10803;
RA Sands J.F., Regnier P., Cummings H.S., Grunberg-Manago M., Hershey J.W.B.;
RT "The existence of two genes between infB and rpsO in the Escherichia coli
RT genome: DNA sequencing and S1 nuclease mapping.";
RL Nucleic Acids Res. 16:10803-10816(1988).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-20, PROTEIN SEQUENCE OF 6-20,
RP FUNCTION, CATALYTIC ACTIVITY, AND CHARACTERIZATION.
RX PubMed=7489483;
RA Nurse K., Wrzesisnski J., Bakin A., Lane B.G., Ofengand J.;
RT "Purification, cloning, and properties of the tRNA psi 55 synthase from
RT Escherichia coli.";
RL RNA 1:102-112(1995).
RN [5]
RP MUTAGENESIS OF CYS-58; CYS-174 AND CYS-193.
RC STRAIN=BLR-DE3, and K12 / JM109 / ATCC 53323;
RX PubMed=10529181; DOI=10.1021/bi9913911;
RA Ramamurthy V., Swann S.L., Spedaliere C.J., Mueller E.G.;
RT "Role of cysteine residues in pseudouridine synthases of different
RT families.";
RL Biochemistry 38:13106-13111(1999).
RN [6]
RP MUTAGENESIS OF LYS-19 AND PRO-20.
RC STRAIN=BLR-DE3;
RX PubMed=10924141; DOI=10.1021/bi001079n;
RA Spedaliere C.J., Hamilton C.S., Mueller E.G.;
RT "Functional importance of motif I of pseudouridine synthases: mutagenesis
RT of aligned lysine and proline residues.";
RL Biochemistry 39:9459-9465(2000).
RN [7]
RP FUNCTION, AND MUTAGENESIS OF ASP-48.
RC STRAIN=BLR-DE3, and K12 / MG1655 / ATCC 47076;
RX PubMed=11142385; DOI=10.1017/s1355838200001588;
RA Gutgsell N., Englund N., Niu L., Kaya Y., Lane B.G., Ofengand J.;
RT "Deletion of the Escherichia coli pseudouridine synthase gene truB blocks
RT formation of pseudouridine 55 in tRNA in vivo, does not affect exponential
RT growth, but confers a strong selective disadvantage in competition with
RT wild-type cells.";
RL RNA 6:1870-1881(2000).
RN [8]
RP BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF HIS-43.
RX PubMed=15581587; DOI=10.1016/j.abb.2004.09.009;
RA Hamilton C.S., Spedaliere C.J., Ginter J.M., Johnston M.V., Mueller E.G.;
RT "The roles of the essential Asp-48 and highly conserved His-43 elucidated
RT by the pH dependence of the pseudouridine synthase TruB.";
RL Arch. Biochem. Biophys. 433:322-334(2005).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 10-314 IN COMPLEX WITH RNA, AND
RP ACTIVE SITE.
RX PubMed=11779468; DOI=10.1016/s0092-8674(01)00618-3;
RA Hoang C., Ferre-D'Amare A.R.;
RT "Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide
RT flipping by an RNA-modifying enzyme.";
RL Cell 107:929-939(2001).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 1-314.
RX PubMed=14566049; DOI=10.1073/pnas.2135585100;
RA Pan H., Agarwalla S., Moustakas D.T., Finer-Moore J., Stroud R.M.;
RT "Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA
RT recognition through a combination of rigid docking and induced fit.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:12648-12653(2003).
CC -!- FUNCTION: Responsible for synthesis of pseudouridine from uracil-55 in
CC the psi GC loop of transfer RNAs. {ECO:0000255|HAMAP-Rule:MF_01080,
CC ECO:0000269|PubMed:11142385, ECO:0000269|PubMed:7489483}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=uridine(55) in tRNA = pseudouridine(55) in tRNA;
CC Xref=Rhea:RHEA:42532, Rhea:RHEA-COMP:10101, Rhea:RHEA-COMP:10102,
CC ChEBI:CHEBI:65314, ChEBI:CHEBI:65315; EC=5.4.99.25;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01080,
CC ECO:0000269|PubMed:7489483};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=148 nM for tRNA (at pH 7.5) {ECO:0000269|PubMed:15581587};
CC -!- INDUCTION: Weakly expressed in maxicells, part of the metY operon that
CC extends to pnp (PubMed:2849753). {ECO:0000269|PubMed:2849753}.
CC -!- SIMILARITY: Belongs to the pseudouridine synthase TruB family. Type 1
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01080, ECO:0000305}.
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DR EMBL; X13270; CAA31635.1; -; Genomic_DNA.
DR EMBL; X13775; CAA32021.1; -; Genomic_DNA.
DR EMBL; U18997; AAA57969.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76200.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77212.1; -; Genomic_DNA.
DR EMBL; S79856; AAB35645.1; -; Genomic_DNA.
DR PIR; S01916; Q9EC35.
DR RefSeq; NP_417635.1; NC_000913.3.
DR RefSeq; WP_000089698.1; NZ_STEB01000012.1.
DR PDB; 1K8W; X-ray; 1.85 A; A=7-314.
DR PDB; 1R3F; X-ray; 1.85 A; A=1-314.
DR PDB; 1ZL3; X-ray; 2.80 A; A=10-314.
DR PDBsum; 1K8W; -.
DR PDBsum; 1R3F; -.
DR PDBsum; 1ZL3; -.
DR AlphaFoldDB; P60340; -.
DR SMR; P60340; -.
DR IntAct; P60340; 5.
DR STRING; 511145.b3166; -.
DR jPOST; P60340; -.
DR PaxDb; P60340; -.
DR PRIDE; P60340; -.
DR EnsemblBacteria; AAC76200; AAC76200; b3166.
DR EnsemblBacteria; BAE77212; BAE77212; BAE77212.
DR GeneID; 66672932; -.
DR GeneID; 947687; -.
DR KEGG; ecj:JW3135; -.
DR KEGG; eco:b3166; -.
DR PATRIC; fig|1411691.4.peg.3564; -.
DR EchoBASE; EB1164; -.
DR eggNOG; COG0130; Bacteria.
DR HOGENOM; CLU_032087_0_3_6; -.
DR InParanoid; P60340; -.
DR OMA; ELQFIRW; -.
DR PhylomeDB; P60340; -.
DR BioCyc; EcoCyc:EG11177-MON; -.
DR BioCyc; MetaCyc:EG11177-MON; -.
DR BRENDA; 5.4.99.25; 2026.
DR EvolutionaryTrace; P60340; -.
DR PRO; PR:P60340; -.
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:0000049; F:tRNA binding; IDA:EcoCyc.
DR GO; GO:0106029; F:tRNA pseudouridine synthase activity; IDA:EcoCyc.
DR GO; GO:1990481; P:mRNA pseudouridine synthesis; IBA:GO_Central.
DR GO; GO:0061818; P:tRNA folding; IMP:EcoCyc.
DR GO; GO:0006400; P:tRNA modification; IBA:GO_Central.
DR GO; GO:0031119; P:tRNA pseudouridine synthesis; IMP:EcoCyc.
DR CDD; cd02573; PseudoU_synth_EcTruB; 1.
DR DisProt; DP03060; -.
DR Gene3D; 2.30.130.10; -; 1.
DR HAMAP; MF_01080; TruB_bact; 1.
DR InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR InterPro; IPR002501; PsdUridine_synth_N.
DR InterPro; IPR015947; PUA-like_sf.
DR InterPro; IPR036974; PUA_sf.
DR InterPro; IPR014780; tRNA_psdUridine_synth_TruB.
DR InterPro; IPR015240; tRNA_sdUridine_synth_fam1_C.
DR InterPro; IPR032819; TruB_C.
DR PANTHER; PTHR13767; PTHR13767; 1.
DR Pfam; PF09157; TruB-C_2; 1.
DR Pfam; PF16198; TruB_C_2; 1.
DR Pfam; PF01509; TruB_N; 1.
DR SUPFAM; SSF55120; SSF55120; 1.
DR SUPFAM; SSF88697; SSF88697; 1.
DR TIGRFAMs; TIGR00431; TruB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Isomerase; Reference proteome;
KW tRNA processing.
FT CHAIN 1..314
FT /note="tRNA pseudouridine synthase B"
FT /id="PRO_0000121830"
FT REGION 124..152
FT /note="RNA binding"
FT /evidence="ECO:0000250"
FT ACT_SITE 48
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01080,
FT ECO:0000305|PubMed:11779468"
FT BINDING 43
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01080,
FT ECO:0000305|PubMed:11779468"
FT BINDING 76
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01080,
FT ECO:0000305|PubMed:11779468"
FT BINDING 179
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01080,
FT ECO:0000305|PubMed:11779468"
FT BINDING 202
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01080,
FT ECO:0000305|PubMed:11779468"
FT MUTAGEN 19
FT /note="K->M,R: Reduced structural stability and decrease in
FT activity."
FT /evidence="ECO:0000269|PubMed:10924141"
FT MUTAGEN 20
FT /note="P->G,L: Reduced structural stability and no change
FT in activity."
FT /evidence="ECO:0000269|PubMed:10924141"
FT MUTAGEN 43
FT /note="H->A: 330-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:15581587"
FT MUTAGEN 43
FT /note="H->F: 2-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:15581587"
FT MUTAGEN 43
FT /note="H->G: 250-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:15581587"
FT MUTAGEN 43
FT /note="H->N: 180-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:15581587"
FT MUTAGEN 43
FT /note="H->Q: 50-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:15581587"
FT MUTAGEN 48
FT /note="D->C: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11142385"
FT MUTAGEN 58
FT /note="C->A: Slight increase in activity. Slight increase
FT in activity; when associated with A-174 and A-193."
FT /evidence="ECO:0000269|PubMed:10529181"
FT MUTAGEN 174
FT /note="C->A: Slight increase in activity. Slight increase
FT in activity; when associated with A-58 and A-193."
FT /evidence="ECO:0000269|PubMed:10529181"
FT MUTAGEN 193
FT /note="C->A: Slight increase in activity; when associated
FT with A-58 and A-174."
FT /evidence="ECO:0000269|PubMed:10529181"
FT MUTAGEN 193
FT /note="C->V: Slight increase in activity."
FT /evidence="ECO:0000269|PubMed:10529181"
FT STRAND 13..19
FT /evidence="ECO:0007829|PDB:1K8W"
FT HELIX 25..35
FT /evidence="ECO:0007829|PDB:1K8W"
FT STRAND 41..45
FT /evidence="ECO:0007829|PDB:1K8W"
FT STRAND 52..59
FT /evidence="ECO:0007829|PDB:1K8W"
FT HELIX 60..66
FT /evidence="ECO:0007829|PDB:1K8W"
FT HELIX 67..70
FT /evidence="ECO:0007829|PDB:1K8W"
FT STRAND 74..82
FT /evidence="ECO:0007829|PDB:1K8W"
FT STRAND 84..90
FT /evidence="ECO:0007829|PDB:1K8W"
FT STRAND 95..98
FT /evidence="ECO:0007829|PDB:1K8W"
FT HELIX 105..113
FT /evidence="ECO:0007829|PDB:1K8W"
FT STRAND 116..121
FT /evidence="ECO:0007829|PDB:1K8W"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:1K8W"
FT HELIX 136..141
FT /evidence="ECO:0007829|PDB:1K8W"
FT STRAND 151..164
FT /evidence="ECO:0007829|PDB:1K8W"
FT STRAND 167..174
FT /evidence="ECO:0007829|PDB:1K8W"
FT HELIX 180..190
FT /evidence="ECO:0007829|PDB:1K8W"
FT STRAND 195..205
FT /evidence="ECO:0007829|PDB:1K8W"
FT HELIX 210..212
FT /evidence="ECO:0007829|PDB:1K8W"
FT HELIX 216..228
FT /evidence="ECO:0007829|PDB:1K8W"
FT HELIX 234..237
FT /evidence="ECO:0007829|PDB:1K8W"
FT HELIX 238..240
FT /evidence="ECO:0007829|PDB:1K8W"
FT HELIX 246..248
FT /evidence="ECO:0007829|PDB:1K8W"
FT STRAND 253..256
FT /evidence="ECO:0007829|PDB:1K8W"
FT HELIX 258..264
FT /evidence="ECO:0007829|PDB:1K8W"
FT TURN 265..267
FT /evidence="ECO:0007829|PDB:1K8W"
FT STRAND 277..285
FT /evidence="ECO:0007829|PDB:1K8W"
FT TURN 286..289
FT /evidence="ECO:0007829|PDB:1K8W"
FT STRAND 290..297
FT /evidence="ECO:0007829|PDB:1K8W"
FT STRAND 303..308
FT /evidence="ECO:0007829|PDB:1K8W"
SQ SEQUENCE 314 AA; 35087 MW; FEA46C01E0E8E7A5 CRC64;
MSRPRRRGRD INGVLLLDKP QGMSSNDALQ KVKRIYNANR AGHTGALDPL ATGMLPICLG
EATKFSQYLL DSDKRYRVIA RLGQRTDTSD ADGQIVEERP VTFSAEQLAA ALDTFRGDIE
QIPSMYSALK YQGKKLYEYA RQGIEVPREA RPITVYELLF IRHEGNELEL EIHCSKGTYI
RTIIDDLGEK LGCGAHVIYL RRLAVSKYPV ERMVTLEHLR ELVEQAEQQD IPAAELLDPL
LMPMDSPASD YPVVNLPLTS SVYFKNGNPV RTSGAPLEGL VRVTEGENGK FIGMGEIDDE
GRVAPRRLVV EYPA
