NSUN6_PYRHO
ID NSUN6_PYRHO Reviewed; 389 AA.
AC O57712;
DT 13-NOV-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=tRNA (cytosine(72)-C(5))-methyltransferase {ECO:0000305|PubMed:30541086};
DE Short=tRNA:m(5)C72 MTase {ECO:0000303|PubMed:30541086};
DE EC=2.1.1.- {ECO:0000269|PubMed:30541086};
DE AltName: Full=PhNSun6 {ECO:0000303|PubMed:30541086};
GN OrderedLocusNames=PH1991 {ECO:0000312|EMBL:BAA31118.1};
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2] {ECO:0007744|PDB:5ZVD, ECO:0007744|PDB:5ZVE, ECO:0007744|PDB:5ZVG}
RP X-RAY CRYSTALLOGRAPHY (2.18 ANGSTROMS) OF 5-388 OF APOENZYME AND IN
RP COMPLEXES WITH S-ADENOSYLMETHIONINE; S-ADENOSYL-L-HOMOCYSTEINE AND SAM
RP ANALOG, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=30541086; DOI=10.1093/nar/gky1236;
RA Li J., Li H., Long T., Dong H., Wang E.D., Liu R.J.;
RT "Archaeal NSUN6 catalyzes m5C72 modification on a wide-range of specific
RT tRNAs.";
RL Nucleic Acids Res. 47:2041-2055(2019).
CC -!- FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that
CC specifically methylates the C5 position of cytosine 72 in several
CC tRNAs. This modification appears to slightly promote the thermal
CC stability of P.horikoshii tRNAs, but does not affect their amino acid
CC accepting activity. Four elements in the acceptor stems of tRNAs are
CC essential for substrate recognition by this enzyme: the target site
CC C72, the 3'-CCA terminus, U73 or G73, and the second base pair C2:G71.
CC {ECO:0000269|PubMed:30541086}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(72) in tRNA + S-adenosyl-L-methionine = 5-
CC methylcytidine(72) in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:61988, Rhea:RHEA-COMP:15996, Rhea:RHEA-COMP:15997,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000269|PubMed:30541086};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:61989;
CC Evidence={ECO:0000305|PubMed:30541086};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(72) in tRNA(Thr) + S-adenosyl-L-methionine = 5-
CC methylcytidine(72) in tRNA(Thr) + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:21124, Rhea:RHEA-COMP:15877, Rhea:RHEA-COMP:15878,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000269|PubMed:30541086};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:21125;
CC Evidence={ECO:0000305|PubMed:30541086};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(72) in tRNA(Cys) + S-adenosyl-L-methionine = 5-
CC methylcytidine(72) in tRNA(Cys) + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:61584, Rhea:RHEA-COMP:15875, Rhea:RHEA-COMP:15876,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000269|PubMed:30541086};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:61585;
CC Evidence={ECO:0000305|PubMed:30541086};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.38 uM for tRNA(Cys)(GCA) {ECO:0000269|PubMed:30541086};
CC KM=0.43 uM for tRNA(Thr)(CGU) {ECO:0000269|PubMed:30541086};
CC KM=0.63 uM for tRNA(Thr)(GGU) {ECO:0000269|PubMed:30541086};
CC KM=0.59 uM for tRNA(Thr)(GGU) {ECO:0000269|PubMed:30541086};
CC KM=0.83 uM for tRNA(Ser)(UGA) {ECO:0000269|PubMed:30541086};
CC KM=0.76 uM for tRNA(Ser)(CGA) {ECO:0000269|PubMed:30541086};
CC KM=0.64 uM for tRNA(Ser)(GGA) {ECO:0000269|PubMed:30541086};
CC KM=0.56 uM for tRNA(Ser)(GCU) {ECO:0000269|PubMed:30541086};
CC KM=0.70 uM for tRNA(Asn)(GUU) {ECO:0000269|PubMed:30541086};
CC KM=0.30 uM for tRNA(Asp)(GUC) {ECO:0000269|PubMed:30541086};
CC KM=0.52 uM for tRNA(Arg)(GCG) {ECO:0000269|PubMed:30541086};
CC Note=kcat is 3.04 min(-1) with tRNA(Cys)(GCA) as substrate. kcat is
CC 4.30 min(-1) with tRNA(Thr)(CGU) as substrate. kcat is 4.34 min(-1)
CC with tRNA(Thr)(GGU) as substrate. kcat is 4.43 min(-1) with
CC tRNA(Thr)(GGU) as substrate. kcat is 2.23 min(-1) with tRNA(Ser)(UGA)
CC as substrate. kcat is 1.50 min(-1) with tRNA(Ser)(CGA) as substrate.
CC kcat is 1.19 min(-1) with tRNA(Ser)(GGA) as substrate. kcat is 0.37
CC min(-1) with tRNA(Ser)(GCU) as substrate. kcat is 1.76 min(-1) with
CC tRNA(Asn)(GUU) as substrate. kcat is 3.71 min(-1) with tRNA(Asp)(GUC)
CC as substrate. kcat is 0.67 min(-1) with tRNA(Arg)(GCG) as substrate.
CC {ECO:0000269|PubMed:30541086};
CC Temperature dependence:
CC Methyltransferase activity is much more higher at 65 degrees Celsius
CC than at 55 and 37 degrees Celsius. {ECO:0000269|PubMed:30541086};
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RsmB/NOP family. {ECO:0000255|HAMAP-Rule:MF_02237}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; BA000001; BAA31118.1; -; Genomic_DNA.
DR PIR; G71215; G71215.
DR PDB; 5ZVD; X-ray; 2.59 A; A/B=5-388.
DR PDB; 5ZVE; X-ray; 2.18 A; A/B=5-388.
DR PDB; 5ZVG; X-ray; 2.50 A; A/B=5-388.
DR PDB; 5ZVH; X-ray; 2.50 A; A/B=5-388.
DR PDBsum; 5ZVD; -.
DR PDBsum; 5ZVE; -.
DR PDBsum; 5ZVG; -.
DR PDBsum; 5ZVH; -.
DR AlphaFoldDB; O57712; -.
DR SMR; O57712; -.
DR STRING; 70601.3258435; -.
DR EnsemblBacteria; BAA31118; BAA31118; BAA31118.
DR KEGG; pho:PH1991; -.
DR eggNOG; arCOG00973; Archaea.
DR eggNOG; arCOG00986; Archaea.
DR OMA; YQGAMLY; -.
DR BRENDA; 2.1.1.202; 5244.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0016428; F:tRNA (cytosine-5-)-methyltransferase activity; IDA:UniProtKB.
DR GO; GO:0000049; F:tRNA binding; IDA:UniProtKB.
DR GO; GO:0006400; P:tRNA modification; IDA:UniProtKB.
DR Gene3D; 2.30.130.10; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR HAMAP; MF_02237; NSUN6; 1.
DR InterPro; IPR001678; MeTrfase_RsmB/NOP2.
DR InterPro; IPR011023; Nop2p.
DR InterPro; IPR043699; NSUN6.
DR InterPro; IPR002478; PUA.
DR InterPro; IPR015947; PUA-like_sf.
DR InterPro; IPR036974; PUA_sf.
DR InterPro; IPR023267; RCMT.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR004521; Uncharacterised_CHP00451.
DR PANTHER; PTHR22807; PTHR22807; 1.
DR Pfam; PF01189; Methyltr_RsmB-F; 1.
DR Pfam; PF01472; PUA; 1.
DR PRINTS; PR02008; RCMTFAMILY.
DR SMART; SM00359; PUA; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR SUPFAM; SSF88697; SSF88697; 1.
DR TIGRFAMs; TIGR00446; nop2p; 1.
DR TIGRFAMs; TIGR00451; unchar_dom_2; 1.
DR PROSITE; PS50890; PUA; 1.
DR PROSITE; PS51686; SAM_MT_RSMB_NOP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Methyltransferase; RNA-binding; S-adenosyl-L-methionine;
KW Transferase.
FT CHAIN 1..389
FT /note="tRNA (cytosine(72)-C(5))-methyltransferase"
FT /id="PRO_0000448570"
FT DOMAIN 92..167
FT /note="PUA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00161"
FT ACT_SITE 327
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 209..215
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023,
FT ECO:0000269|PubMed:30541086"
FT BINDING 233
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023,
FT ECO:0000269|PubMed:30541086"
FT BINDING 238
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:30541086"
FT BINDING 260
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023,
FT ECO:0000269|PubMed:30541086"
FT BINDING 277
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023,
FT ECO:0000269|PubMed:30541086"
FT BINDING 304
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:30541086"
FT HELIX 6..8
FT /evidence="ECO:0007829|PDB:5ZVE"
FT HELIX 11..21
FT /evidence="ECO:0007829|PDB:5ZVE"
FT HELIX 23..33
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 38..44
FT /evidence="ECO:0007829|PDB:5ZVE"
FT TURN 46..48
FT /evidence="ECO:0007829|PDB:5ZVE"
FT HELIX 51..60
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 74..78
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 94..97
FT /evidence="ECO:0007829|PDB:5ZVE"
FT HELIX 99..105
FT /evidence="ECO:0007829|PDB:5ZVE"
FT TURN 106..108
FT /evidence="ECO:0007829|PDB:5ZVE"
FT HELIX 113..115
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 116..119
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 128..132
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 138..146
FT /evidence="ECO:0007829|PDB:5ZVE"
FT HELIX 148..151
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 155..168
FT /evidence="ECO:0007829|PDB:5ZVE"
FT HELIX 176..179
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 183..185
FT /evidence="ECO:0007829|PDB:5ZVE"
FT HELIX 188..197
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 205..209
FT /evidence="ECO:0007829|PDB:5ZVE"
FT HELIX 214..222
FT /evidence="ECO:0007829|PDB:5ZVE"
FT TURN 223..225
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 229..234
FT /evidence="ECO:0007829|PDB:5ZVE"
FT HELIX 236..249
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 253..259
FT /evidence="ECO:0007829|PDB:5ZVE"
FT HELIX 261..266
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 271..277
FT /evidence="ECO:0007829|PDB:5ZVE"
FT HELIX 295..314
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 316..327
FT /evidence="ECO:0007829|PDB:5ZVE"
FT TURN 332..334
FT /evidence="ECO:0007829|PDB:5ZVE"
FT HELIX 335..343
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 346..348
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 356..359
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 362..368
FT /evidence="ECO:0007829|PDB:5ZVE"
FT HELIX 370..373
FT /evidence="ECO:0007829|PDB:5ZVE"
FT STRAND 378..385
FT /evidence="ECO:0007829|PDB:5ZVE"
SQ SEQUENCE 389 AA; 44284 MW; 90303398D603E5A7 CRC64;
MAMNYLEAFP KELREYYKNL FGKEEANKIM KKLREPVEHY YIRVNTLKIS REKLIGELKK
EGLKPLRSPY LPEGLYFVRE GPNFSDDFEP KLPVVVANKY AAESVYQGAM LYAPGVLKAD
KNIKEGDEVQ IRDPKGLLVG IGIARMDYKE MTEATRGLAV EVTLPKFKLP SLSELKAFEK
GYFYPQGLPS MVTARVLEPK EDDVIIDMAA APGGKTTHIA QLLENKGEII AIDKSKNRLR
KMEENIKRLG VKNVKLVQMD ARKLPDLGIK ADKILLDAPC TALGVRPKLW EERTLKHIEA
TARYQRAFIW AAIKSLRRGG VLVYSTCTLS YEENEGNVKF MIRKGMKLEE QSIFIGSPGI
GMNKVQRFYP HKHLTQGFFI AKLRKVKDI
