TRUB_THEMA
ID TRUB_THEMA Reviewed; 309 AA.
AC Q9WZW0;
DT 04-MAY-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 25-MAY-2022, entry version 146.
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};
DE AltName: Full=tRNA pseudouridine(55) synthase {ECO:0000255|HAMAP-Rule:MF_01080, ECO:0000303|PubMed:12499554};
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 {ECO:0000255|HAMAP-Rule:MF_01080, ECO:0000303|PubMed:14566049};
GN OrderedLocusNames=TM_0856;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP CRYSTALLIZATION.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=12499554; DOI=10.1107/s0907444902018292;
RA Wouters J., Tricot C., Durbecq V., Roovers M., Stalon V., Droogmans L.;
RT "Preliminary X-ray crystallographic analysis of tRNA pseudouridine 55
RT synthase from the thermophilic eubacterium Thermotoga maritima.";
RL Acta Crystallogr. D 59:152-154(2003).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF COMPLEX WITH RNA.
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 -!- 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 -!- SIMILARITY: Belongs to the pseudouridine synthase TruB family. Type 1
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01080}.
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DR EMBL; AE000512; AAD35938.1; -; Genomic_DNA.
DR PIR; A72325; A72325.
DR RefSeq; NP_228665.1; NC_000853.1.
DR RefSeq; WP_004080766.1; NZ_CP011107.1.
DR PDB; 1R3E; X-ray; 2.10 A; A=1-309.
DR PDB; 1ZE1; X-ray; 2.90 A; A/B/C/D=1-309.
DR PDB; 1ZE2; X-ray; 3.00 A; A/B=1-309.
DR PDB; 2AB4; X-ray; 2.40 A; A=1-309.
DR PDBsum; 1R3E; -.
DR PDBsum; 1ZE1; -.
DR PDBsum; 1ZE2; -.
DR PDBsum; 2AB4; -.
DR AlphaFoldDB; Q9WZW0; -.
DR SMR; Q9WZW0; -.
DR STRING; 243274.THEMA_00355; -.
DR EnsemblBacteria; AAD35938; AAD35938; TM_0856.
DR KEGG; tma:TM0856; -.
DR eggNOG; COG0130; Bacteria.
DR InParanoid; Q9WZW0; -.
DR OMA; ELQFIRW; -.
DR OrthoDB; 1166299at2; -.
DR BRENDA; 5.4.99.25; 6331.
DR EvolutionaryTrace; Q9WZW0; -.
DR Proteomes; UP000008183; Chromosome.
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; IEA:UniProtKB-EC.
DR GO; GO:1990481; P:mRNA pseudouridine synthesis; IBA:GO_Central.
DR GO; GO:0006400; P:tRNA modification; IBA:GO_Central.
DR GO; GO:0031119; P:tRNA pseudouridine synthesis; IEA:UniProtKB-UniRule.
DR CDD; cd02573; PseudoU_synth_EcTruB; 1.
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; IPR002478; PUA.
DR InterPro; IPR015947; PUA-like_sf.
DR InterPro; IPR036974; PUA_sf.
DR InterPro; IPR014780; tRNA_psdUridine_synth_TruB.
DR InterPro; IPR032819; TruB_C.
DR PANTHER; PTHR13767; PTHR13767; 1.
DR Pfam; PF01472; PUA; 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.
DR PROSITE; PS50890; PUA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Isomerase; Reference proteome; tRNA processing.
FT CHAIN 1..309
FT /note="tRNA pseudouridine synthase B"
FT /id="PRO_0000121929"
FT DOMAIN 229..306
FT /note="PUA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01080"
FT ACT_SITE 39
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01080"
FT STRAND 4..10
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 12..14
FT /evidence="ECO:0007829|PDB:1R3E"
FT HELIX 16..26
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 32..36
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 43..50
FT /evidence="ECO:0007829|PDB:1R3E"
FT HELIX 51..60
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 65..73
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 75..81
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 86..89
FT /evidence="ECO:0007829|PDB:1R3E"
FT HELIX 96..104
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 105..112
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 116..119
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 121..126
FT /evidence="ECO:0007829|PDB:2AB4"
FT HELIX 127..132
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:1ZE1"
FT STRAND 142..155
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 158..165
FT /evidence="ECO:0007829|PDB:1R3E"
FT HELIX 171..181
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 186..196
FT /evidence="ECO:0007829|PDB:1R3E"
FT HELIX 201..203
FT /evidence="ECO:0007829|PDB:1R3E"
FT TURN 207..209
FT /evidence="ECO:0007829|PDB:1R3E"
FT HELIX 212..218
FT /evidence="ECO:0007829|PDB:1R3E"
FT HELIX 222..224
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 231..233
FT /evidence="ECO:0007829|PDB:1R3E"
FT TURN 236..238
FT /evidence="ECO:0007829|PDB:1R3E"
FT HELIX 239..242
FT /evidence="ECO:0007829|PDB:1R3E"
FT TURN 243..245
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 248..252
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 253..255
FT /evidence="ECO:0007829|PDB:1ZE1"
FT STRAND 264..268
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 270..272
FT /evidence="ECO:0007829|PDB:1R3E"
FT STRAND 274..282
FT /evidence="ECO:0007829|PDB:1R3E"
FT HELIX 287..290
FT /evidence="ECO:0007829|PDB:1ZE1"
FT STRAND 291..294
FT /evidence="ECO:0007829|PDB:1ZE1"
FT STRAND 298..305
FT /evidence="ECO:0007829|PDB:1R3E"
SQ SEQUENCE 309 AA; 35459 MW; 04825FD6D643CE9C CRC64;
MKHGILVAYK PKGPTSHDVV DEVRKKLKTR KVGHGGTLDP FACGVLIIGV NQGTRILEFY
KDLKKVYWVK MRLGLITETF DITGEVVEER ECNVTEEEIR EAIFSFVGEY DQVPPAYSAK
KYKGERLYKL AREGKIINLP PKRVKIFKIW DVNIEGRDVS FRVEVSPGTY IRSLCMDIGY
KLGCGATAVE LVRESVGPHT IEESLNVFEA APEEIENRII PLEKCLEWLP RVVVHQESTK
MILNGSQIHL EMLKEWDGFK KGEVVRVFNE EGRLLALAEA ERNSSFLETL RKHERNERVL
TLRKVFNTR
