TRM13_DICDI
ID TRM13_DICDI Reviewed; 525 AA.
AC Q54BD5;
DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 84.
DE RecName: Full=tRNA:m(4)X modification enzyme TRM13 homolog;
DE EC=2.1.1.225;
GN Name=trm13; ORFNames=DDB_G0293682;
OS Dictyostelium discoideum (Slime mold).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
CC -!- FUNCTION: tRNA methylase which 2'-O-methylates cytidine(4) in tRNA(Pro)
CC and tRNA(Gly)(GCC), and adenosine(4) in tRNA(His).
CC {ECO:0000250|UniProtKB:Q12383}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(4) in tRNA(Pro) + S-adenosyl-L-methionine = 2'-O-
CC methylcytidine(4) in tRNA(Pro) + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:32767, Rhea:RHEA-COMP:10397, Rhea:RHEA-COMP:10398,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74495, ChEBI:CHEBI:82748; EC=2.1.1.225;
CC Evidence={ECO:0000250|UniProtKB:Q12383};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(4) in tRNA(Gly)(GCC) + S-adenosyl-L-methionine = 2'-
CC O-methylcytidine(4) in tRNA(Gly)(GCC) + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:43192, Rhea:RHEA-COMP:10399, Rhea:RHEA-
CC COMP:10400, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74495, ChEBI:CHEBI:82748; EC=2.1.1.225;
CC Evidence={ECO:0000250|UniProtKB:Q12383};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(4) in tRNA(His) + S-adenosyl-L-methionine = 2'-O-
CC methyladenosine(4) in tRNA(His) + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:43196, Rhea:RHEA-COMP:10401, Rhea:RHEA-COMP:10402,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74477; EC=2.1.1.225;
CC Evidence={ECO:0000250|UniProtKB:Q12383};
CC -!- SIMILARITY: Belongs to the methyltransferase TRM13 family.
CC {ECO:0000305}.
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DR EMBL; AAFI02000218; EAL60653.1; -; Genomic_DNA.
DR RefSeq; XP_629094.1; XM_629092.1.
DR AlphaFoldDB; Q54BD5; -.
DR STRING; 44689.DDB0192091; -.
DR PaxDb; Q54BD5; -.
DR EnsemblProtists; EAL60653; EAL60653; DDB_G0293682.
DR GeneID; 8629387; -.
DR KEGG; ddi:DDB_G0293682; -.
DR dictyBase; DDB_G0293682; -.
DR eggNOG; KOG2811; Eukaryota.
DR HOGENOM; CLU_027610_1_0_1; -.
DR InParanoid; Q54BD5; -.
DR OMA; HRCSWRS; -.
DR PhylomeDB; Q54BD5; -.
DR PRO; PR:Q54BD5; -.
DR Proteomes; UP000002195; Chromosome 6.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0106050; F:tRNA 2'-O-methyltransferase activity; IEA:InterPro.
DR GO; GO:0008175; F:tRNA methyltransferase activity; IBA:GO_Central.
DR GO; GO:0030488; P:tRNA methylation; IBA:GO_Central.
DR InterPro; IPR007871; Methyltransferase_TRM13.
DR InterPro; IPR039044; Trm13.
DR InterPro; IPR022776; TRM13/UPF0224_CHHC_Znf_dom.
DR InterPro; IPR021721; Znf_CCCH-type_TRM13.
DR PANTHER; PTHR12998; PTHR12998; 1.
DR Pfam; PF05206; TRM13; 1.
DR Pfam; PF11722; zf-TRM13_CCCH; 1.
DR Pfam; PF05253; zf-U11-48K; 1.
DR PROSITE; PS51800; ZF_CHHC_U11_48K; 1.
PE 3: Inferred from homology;
KW Coiled coil; Metal-binding; Methyltransferase; Reference proteome;
KW S-adenosyl-L-methionine; Transferase; tRNA processing; Zinc; Zinc-finger.
FT CHAIN 1..525
FT /note="tRNA:m(4)X modification enzyme TRM13 homolog"
FT /id="PRO_0000339430"
FT ZN_FING 137..164
FT /note="CHHC U11-48K-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT REGION 31..50
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 91..137
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 440..469
FT /evidence="ECO:0000255"
FT COMPBIAS 92..127
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 140
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT BINDING 146
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT BINDING 156
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT BINDING 160
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
SQ SEQUENCE 525 AA; 61425 MW; 0D70C667064584A3 CRC64;
MGEINNNKEI NEKDDEINNK RLKYEGFIKK EKKKKQKIDH SIPLKEKPTQ EDIDSHSECL
FWIVNKKKHR AEFCKYKRAK DSILCNHHKP IDQISSEPQP QLTDYNGDDV TENNNNSTTT
TTATTQDDNS KPKERKRIHC PLNPTHIIYE CKLQKHLKAC PNAKVGQKNA HIELSKKEPY
YKENINDLNE NVKLTLEPII LSQVSTENLI NISIKLDQFF EKFFKNEIQS LNQTHKSFDK
IFNSDQQLKH IQQESSIINL LENSNLYNSD NVYLEFGAGS GKLSNHIFMS HEKKSGHILI
DRMKFRSLKK VDRLIKNEKG CHHFSRLLID IRHLNLSNLS ILEEKPFVIT SKHLCGCATD
FTLDSIFNLL NNSNEKVNNN FKGIGIATCC HHICNFNTYS NQSYLKDQLN ITPLEFQLIC
SISSWATIDE NKCNNDDDDN EVEEDDELIK KDKKEKKEFE NQLKIEFNKQ DVFSIKRKEE
LGYKAKRLID YGRYLFIKEK LNLPNTKFWI YTNQSKENLF LVSNK
