TRMI_PYRAB
ID TRMI_PYRAB Reviewed; 253 AA.
AC Q9V1J7; G8ZGD2;
DT 03-MAY-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI;
DE EC=2.1.1.219;
DE AltName: Full=tRNA(m1A57/58)-methyltransferase;
GN Name=trmI; Synonyms=pimT-like; OrderedLocusNames=PYRAB04300;
GN ORFNames=PAB0283;
OS Pyrococcus abyssi (strain GE5 / Orsay).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=272844;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GE5 / Orsay;
RX PubMed=12622808; DOI=10.1046/j.1365-2958.2003.03381.x;
RA Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O.,
RA Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J.,
RA Weissenbach J., Zivanovic Y., Forterre P.;
RT "An integrated analysis of the genome of the hyperthermophilic archaeon
RT Pyrococcus abyssi.";
RL Mol. Microbiol. 47:1495-1512(2003).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=GE5 / Orsay;
RX PubMed=22057919; DOI=10.1007/s00284-011-0035-x;
RA Gao J., Wang J.;
RT "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and
RT Pyrococcus furiosus DSM 3638.";
RL Curr. Microbiol. 64:118-129(2012).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, DISULFIDE BONDS, AND MUTAGENESIS OF
RP CYS-196 AND CYS-233.
RC STRAIN=GE5 / Orsay;
RX PubMed=14739239; DOI=10.1093/nar/gkh191;
RA Roovers M., Wouters J., Bujnicki J.M., Tricot C., Stalon V., Grosjean H.,
RA Droogmans L.;
RT "A primordial RNA modification enzyme: the case of tRNA (m1A)
RT methyltransferase.";
RL Nucleic Acids Res. 32:465-476(2004).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-HOMOCYSTEINE AND S-ADENOSYL-L-METHIONINE, FUNCTION, CATALYTIC
RP ACTIVITY, SUBUNIT, DISULFIDE BONDS, DOMAIN, AND MUTAGENESIS OF HIS-78.
RX PubMed=20483913; DOI=10.1093/nar/gkq381;
RA Guelorget A., Roovers M., Guerineau V., Barbey C., Li X.,
RA Golinelli-Pimpaneau B.;
RT "Insights into the hyperthermostability and unusual region-specificity of
RT archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase.";
RL Nucleic Acids Res. 38:6206-6218(2010).
CC -!- FUNCTION: Catalyzes the S-adenosyl-L-methionine-dependent formation of
CC N(1)-methyladenosine at position(s) 57 (m1A57) and 58 (m1A58) in the T-
CC loop of some tRNAs. Methylates the first adenine of an AA sequence.
CC {ECO:0000269|PubMed:14739239, ECO:0000269|PubMed:20483913}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(57)/adenosine(58) in tRNA + 2 S-adenosyl-L-
CC methionine = 2 H(+) + N(1)-methyladenosine(57)/N(1)-
CC methyladenosine(58) in tRNA + 2 S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:41740, Rhea:RHEA-COMP:9580, Rhea:RHEA-COMP:9582,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74491; EC=2.1.1.219;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00952,
CC ECO:0000269|PubMed:14739239, ECO:0000269|PubMed:20483913};
CC -!- SUBUNIT: Homotetramer composed of a dimer of dimers; disulfide-linked.
CC Disulfide bonds are important for the stability of TrmI at extreme
CC temperatures. {ECO:0000269|PubMed:14739239,
CC ECO:0000269|PubMed:20483913}.
CC -!- DOMAIN: Contains a large catalytic C-terminal domain that binds S-
CC adenosyl-L-methionine and a smaller N-terminal domain that may play a
CC role in tRNA recognition. Domains are connected by a linker region.
CC {ECO:0000269|PubMed:20483913}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. TRM61 family. {ECO:0000255|PROSITE-ProRule:PRU00952}.
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DR EMBL; AJ248284; CAB49352.1; -; Genomic_DNA.
DR EMBL; HE613800; CCE69811.1; -; Genomic_DNA.
DR PIR; A75159; A75159.
DR RefSeq; WP_010867553.1; NC_000868.1.
DR PDB; 3LGA; X-ray; 2.05 A; A/B/C/D=1-253.
DR PDB; 3LHD; X-ray; 2.59 A; A/B/C/D=1-253.
DR PDB; 3MB5; X-ray; 1.60 A; A=1-253.
DR PDBsum; 3LGA; -.
DR PDBsum; 3LHD; -.
DR PDBsum; 3MB5; -.
DR AlphaFoldDB; Q9V1J7; -.
DR SMR; Q9V1J7; -.
DR STRING; 272844.PAB0283; -.
DR EnsemblBacteria; CAB49352; CAB49352; PAB0283.
DR GeneID; 1495324; -.
DR KEGG; pab:PAB0283; -.
DR PATRIC; fig|272844.11.peg.452; -.
DR eggNOG; arCOG00978; Archaea.
DR HOGENOM; CLU_025402_0_1_2; -.
DR OMA; VVYPKDA; -.
DR OrthoDB; 64860at2157; -.
DR PhylomeDB; Q9V1J7; -.
DR BioCyc; MetaCyc:MON-16690; -.
DR BRENDA; 2.1.1.219; 5242.
DR EvolutionaryTrace; Q9V1J7; -.
DR Proteomes; UP000000810; Chromosome.
DR Proteomes; UP000009139; Chromosome.
DR GO; GO:0031515; C:tRNA (m1A) methyltransferase complex; IEA:InterPro.
DR GO; GO:0016429; F:tRNA (adenine-N1-)-methyltransferase activity; IEA:InterPro.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR014816; tRNA_MeTrfase_Gcd14.
DR PANTHER; PTHR12133; PTHR12133; 1.
DR Pfam; PF08704; GCD14; 1.
DR PIRSF; PIRSF017269; GCD14; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51620; SAM_TRM61; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Disulfide bond; Methyltransferase; S-adenosyl-L-methionine;
KW Transferase; tRNA processing.
FT CHAIN 1..253
FT /note="tRNA (adenine(57)-N(1)/adenine(58)-N(1))-
FT methyltransferase TrmI"
FT /id="PRO_0000407310"
FT BINDING 104..107
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 125
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00952,
FT ECO:0000269|PubMed:20483913"
FT BINDING 153
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00952,
FT ECO:0000269|PubMed:20483913"
FT BINDING 169
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00952,
FT ECO:0000269|PubMed:20483913"
FT DISULFID 196
FT /note="Interchain (with C-233)"
FT DISULFID 233
FT /note="Interchain (with C-196)"
FT MUTAGEN 78
FT /note="H->Y: Decreases efficiency of the dimethylation
FT reaction."
FT /evidence="ECO:0000269|PubMed:20483913"
FT MUTAGEN 196
FT /note="C->S: Decreases stability of TrmI at extreme
FT temperatures; when associated with S-233."
FT /evidence="ECO:0000269|PubMed:14739239"
FT MUTAGEN 233
FT /note="C->S: Decreases stability of TrmI at extreme
FT temperatures; when associated with S-196."
FT /evidence="ECO:0000269|PubMed:14739239"
FT STRAND 7..11
FT /evidence="ECO:0007829|PDB:3MB5"
FT STRAND 17..21
FT /evidence="ECO:0007829|PDB:3MB5"
FT STRAND 24..29
FT /evidence="ECO:0007829|PDB:3MB5"
FT STRAND 32..35
FT /evidence="ECO:0007829|PDB:3MB5"
FT HELIX 36..39
FT /evidence="ECO:0007829|PDB:3MB5"
FT STRAND 47..49
FT /evidence="ECO:0007829|PDB:3MB5"
FT STRAND 55..59
FT /evidence="ECO:0007829|PDB:3MB5"
FT HELIX 63..69
FT /evidence="ECO:0007829|PDB:3MB5"
FT HELIX 79..88
FT /evidence="ECO:0007829|PDB:3MB5"
FT STRAND 96..100
FT /evidence="ECO:0007829|PDB:3MB5"
FT HELIX 106..115
FT /evidence="ECO:0007829|PDB:3MB5"
FT STRAND 119..124
FT /evidence="ECO:0007829|PDB:3MB5"
FT HELIX 128..141
FT /evidence="ECO:0007829|PDB:3MB5"
FT TURN 144..146
FT /evidence="ECO:0007829|PDB:3MB5"
FT STRAND 147..150
FT /evidence="ECO:0007829|PDB:3MB5"
FT HELIX 154..156
FT /evidence="ECO:0007829|PDB:3MB5"
FT STRAND 162..168
FT /evidence="ECO:0007829|PDB:3MB5"
FT HELIX 173..176
FT /evidence="ECO:0007829|PDB:3MB5"
FT HELIX 177..183
FT /evidence="ECO:0007829|PDB:3MB5"
FT STRAND 184..196
FT /evidence="ECO:0007829|PDB:3MB5"
FT HELIX 197..209
FT /evidence="ECO:0007829|PDB:3MB5"
FT HELIX 211..213
FT /evidence="ECO:0007829|PDB:3MB5"
FT STRAND 218..220
FT /evidence="ECO:0007829|PDB:3MB5"
FT STRAND 227..230
FT /evidence="ECO:0007829|PDB:3MB5"
FT STRAND 233..236
FT /evidence="ECO:0007829|PDB:3MB5"
FT STRAND 238..241
FT /evidence="ECO:0007829|PDB:3LGA"
FT STRAND 246..252
FT /evidence="ECO:0007829|PDB:3MB5"
SQ SEQUENCE 253 AA; 28873 MW; AFE9CB4FA59470C1 CRC64;
MIREGDKVVL VDPRGKRYLI TVSKRDFHTD LGILKLEEII GRNFGEAIKS HKGHEFKILR
PRIVDYLDKM KRGPQIVHPK DAALIVAYAG ISPGDFIVEA GVGSGALTLF LANIVGPEGR
VVSYEIREDF AKLAWENIKW AGFDDRVTIK LKDIYEGIEE ENVDHVILDL PQPERVVEHA
AKALKPGGFF VAYTPCSNQV MRLHEKLREF KDYFMKPRTI NVLVFDQEVK KECMRPRTTA
LVHTGYITFA RRI
