TRUD_METMA
ID TRUD_METMA Reviewed; 438 AA.
AC Q8Q0M2;
DT 26-SEP-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 25-MAY-2022, entry version 120.
DE RecName: Full=Probable tRNA pseudouridine synthase D {ECO:0000255|HAMAP-Rule:MF_01082};
DE EC=5.4.99.27 {ECO:0000255|HAMAP-Rule:MF_01082};
DE AltName: Full=tRNA pseudouridine(13) synthase {ECO:0000255|HAMAP-Rule:MF_01082};
DE AltName: Full=tRNA pseudouridylate synthase D {ECO:0000255|HAMAP-Rule:MF_01082};
DE AltName: Full=tRNA-uridine isomerase D {ECO:0000255|HAMAP-Rule:MF_01082};
GN Name=truD {ECO:0000255|HAMAP-Rule:MF_01082}; OrderedLocusNames=MM_0114;
OS Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM
OS 11833 / OCM 88) (Methanosarcina frisia).
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanosarcinales; Methanosarcinaceae; Methanosarcina.
OX NCBI_TaxID=192952;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88;
RX PubMed=12125824;
RA Deppenmeier U., Johann A., Hartsch T., Merkl R., Schmitz R.A.,
RA Martinez-Arias R., Henne A., Wiezer A., Baeumer S., Jacobi C.,
RA Brueggemann H., Lienard T., Christmann A., Boemecke M., Steckel S.,
RA Bhattacharyya A., Lykidis A., Overbeek R., Klenk H.-P., Gunsalus R.P.,
RA Fritz H.-J., Gottschalk G.;
RT "The genome of Methanosarcina mazei: evidence for lateral gene transfer
RT between Bacteria and Archaea.";
RL J. Mol. Microbiol. Biotechnol. 4:453-461(2002).
CC -!- FUNCTION: Could be responsible for synthesis of pseudouridine from
CC uracil-13 in transfer RNAs. {ECO:0000255|HAMAP-Rule:MF_01082}.
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:0000255|HAMAP-Rule:MF_01082};
CC -!- SIMILARITY: Belongs to the pseudouridine synthase TruD family.
CC {ECO:0000255|HAMAP-Rule:MF_01082}.
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DR EMBL; AE008384; AAM29810.1; -; Genomic_DNA.
DR RefSeq; WP_011032068.1; NC_003901.1.
DR PDB; 1Z2Z; X-ray; 2.60 A; A/B=1-438.
DR PDBsum; 1Z2Z; -.
DR AlphaFoldDB; Q8Q0M2; -.
DR SMR; Q8Q0M2; -.
DR STRING; 192952.MM_0114; -.
DR EnsemblBacteria; AAM29810; AAM29810; MM_0114.
DR GeneID; 24838872; -.
DR KEGG; mma:MM_0114; -.
DR PATRIC; fig|192952.21.peg.127; -.
DR eggNOG; arCOG04252; Archaea.
DR HOGENOM; CLU_005281_4_1_2; -.
DR OMA; GFPNYFD; -.
DR EvolutionaryTrace; Q8Q0M2; -.
DR Proteomes; UP000000595; Chromosome.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0106029; F:tRNA pseudouridine synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0031119; P:tRNA pseudouridine synthesis; IEA:UniProtKB-UniRule.
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 PANTHER; PTHR13326; PTHR13326; 1.
DR Pfam; PF01142; TruD; 1.
DR PIRSF; PIRSF037016; Pseudouridin_synth_euk_prd; 1.
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; Isomerase; Reference proteome; tRNA processing.
FT CHAIN 1..438
FT /note="Probable tRNA pseudouridine synthase D"
FT /id="PRO_0000152543"
FT DOMAIN 165..390
FT /note="TRUD"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT ACT_SITE 86
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT HELIX 5..8
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT TURN 9..11
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 30..32
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 33..39
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 47..58
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 61..72
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 76..78
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 79..83
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 87..98
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 102..105
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 113..123
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 130..144
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 146..163
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 165..167
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT TURN 172..175
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 177..179
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 182..191
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 194..202
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 213..223
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 226..232
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 238..249
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 254..258
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 263..287
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 292..294
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 306..308
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 312..314
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT TURN 320..322
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 323..330
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT TURN 331..333
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 336..338
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 343..345
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 352..363
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 368..370
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 377..379
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 387..391
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 398..400
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 408..413
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT STRAND 415..417
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT HELIX 423..430
FT /evidence="ECO:0007829|PDB:1Z2Z"
FT TURN 434..436
FT /evidence="ECO:0007829|PDB:1Z2Z"
SQ SEQUENCE 438 AA; 49499 MW; D8404CC1672C0016 CRC64;
MEVPEIEKQI GINLYSTDTT GLGGQLRQEI EDFIVKEITN REEGEEGKYL IVELTKRDWD
THHLTRTLSR ILQVSQKRIS VAGTKDKRAL TTQKISIFDT DASEIEKIHL KDIELKVLGR
SRKSVELGDL WGNDFRITVR NIENSPEETE ALLKKTTDEI LAQGGVPNFF GIQRFGSVRP
VTHLVGKAIV EGNFEKAALL YIAEPFPEEP EETKNARQFV KDTLDFKEGL KTYPLRLGHE
RAMMNHLIAN PEDYSGSFRV LPQNLYRMFV HGYQSYIYNI ILCRRIEAGI PLNRAVEGDI
VCFRNEVGLP DSSKTEKVTS ETVNAMNRLL KLGRAFITAP LPGYNTEFAS GIPGEIENGV
LKELGVSLEG FNIEKFPEMS SKGTRREVLL EVKPKFEAGE DELNPGKSKA VLEFMLPKGS
YATTVLREYM KVNPLQMS
