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Conserved domains on  [gi|1958659569|ref|XP_038942255|]
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rRNA methyltransferase 3, mitochondrial isoform X2 [Rattus norvegicus]

Protein Classification

TrmH family RNA methyltransferase( domain architecture ID 11426248)

TrmH family RNA methyltransferase catalyzes the methylation of rRNA or tRNA at specific sites in a S-adenosyl-L-methionine (SAM)-dependent manner

CATH:  3.40.1280.10
EC:  2.1.1.-
Gene Ontology:  GO:0008173|GO:0032259|GO:0003723|GO:1904047|GO:0006396
PubMed:  11763972|18029778|17338813|30457841|8265370

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SpoU COG0566
tRNA G18 (ribose-2'-O)-methylase SpoU [Translation, ribosomal structure and biogenesis]; tRNA ...
 112-249 4.79e-29

tRNA G18 (ribose-2'-O)-methylase SpoU [Translation, ribosomal structure and biogenesis]; tRNA G18 (ribose-2'-O)-methylase SpoU is part of the Pathway/BioSystem: tRNA modification


:

Pssm-ID: 440332 [Multi-domain]  Cd Length: 265  Bit Score: 111.06  E-value: 4.79e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659569 112 KSRPFREKQGKILLEGRRLIADALKAGAVPKMFFFS-----RLEYIKELPvdKLKGVSLIKVKFEDIKDWSDLVTPQGIM 186
Cdd:COG0566    16 RDKKYREEEGLFLAEGRHAVEEALKAGREIEELLVTegaldRLAELLALA--KAAGIPVYEVSREVLDKLSGTETHQGVL 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958659569 187 GIFAKPDPVKMTYPETQLHHSlPLLLICDNLRDPGNLGTILRSAAGAGCSKVLLTKGCIYAYS 249
Cdd:COG0566    94 AVVRPPEYADLEDLLAEAGEP-PLLLVLDGVQDPGNLGAILRSAAAFGVDGVILPKRRADPYN 155
 
Name Accession Description Interval E-value
SpoU COG0566
tRNA G18 (ribose-2'-O)-methylase SpoU [Translation, ribosomal structure and biogenesis]; tRNA ...
 112-249 4.79e-29

tRNA G18 (ribose-2'-O)-methylase SpoU [Translation, ribosomal structure and biogenesis]; tRNA G18 (ribose-2'-O)-methylase SpoU is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440332 [Multi-domain]  Cd Length: 265  Bit Score: 111.06  E-value: 4.79e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659569 112 KSRPFREKQGKILLEGRRLIADALKAGAVPKMFFFS-----RLEYIKELPvdKLKGVSLIKVKFEDIKDWSDLVTPQGIM 186
Cdd:COG0566    16 RDKKYREEEGLFLAEGRHAVEEALKAGREIEELLVTegaldRLAELLALA--KAAGIPVYEVSREVLDKLSGTETHQGVL 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958659569 187 GIFAKPDPVKMTYPETQLHHSlPLLLICDNLRDPGNLGTILRSAAGAGCSKVLLTKGCIYAYS 249
Cdd:COG0566    94 AVVRPPEYADLEDLLAEAGEP-PLLLVLDGVQDPGNLGAILRSAAAFGVDGVILPKRRADPYN 155
SpoU-like_RNMTL1 cd18106
SAM-dependent rRNA methylase related to RNMTL1; RNMTL1 (also known as HC90, MRM3 and RMTL1) ...
 210-245 3.19e-18

SAM-dependent rRNA methylase related to RNMTL1; RNMTL1 (also known as HC90, MRM3 and RMTL1) catalyzes the methylation of 2'-O-ribose residues G1370 to GmG residue of the mitochondrial 16S rRNA. RNMTL1 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349979  Cd Length: 148  Bit Score: 79.22  E-value: 3.19e-18
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958659569 210 LLLICDNLRDPGNLGTILRSAAGAGCSKVLLTKGCI 245
Cdd:cd18106     1 LTVICDNIRDPGNLGSILRSAAAAGCSKVLLTKGCV 36
SpoU_sub_bind smart00967
RNA 2'-O ribose methyltransferase substrate binding; This domain is a RNA 2'-O ribose ...
 125-191 2.71e-09

RNA 2'-O ribose methyltransferase substrate binding; This domain is a RNA 2'-O ribose methyltransferase substrate binding domain.


Pssm-ID: 214943 [Multi-domain]  Cd Length: 70  Bit Score: 52.54  E-value: 2.71e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659569  125 LEGRRLIADALKAGAVPKMFFFSRLEYIKELPVDKL---KGVSLIKVKFEDIKDWSDLVTPQGIMGIFAK 191
Cdd:smart00967   1 IEGRHAVEEALKSGRRIKELYLTEGRAERLKELLKLakeRGIKVIEVSKKELDKLSGTANHQGVVAVVKP 70
SpoU_methylase pfam00588
SpoU rRNA Methylase family; This family of proteins probably use S-AdoMet.
 209-249 9.92e-09

SpoU rRNA Methylase family; This family of proteins probably use S-AdoMet.


Pssm-ID: 425768  Cd Length: 142  Bit Score: 52.92  E-value: 9.92e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958659569 209 PLLLICDNLRDPGNLGTILRSAAGAGCSKVLLTK-GCIYAYS 249
Cdd:pfam00588   1 PLVVVLDNIQDPGNLGAIIRTAAAFGADGLILVEpRSADPYN 42
PRK11181 PRK11181
23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB;
187-242 8.43e-06

23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB;


Pssm-ID: 183021 [Multi-domain]  Cd Length: 244  Bit Score: 46.11  E-value: 8.43e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958659569 187 GIFAKPDPVKmTYPETQL-----HHSLPLLLICDNLRDPGNLGTILRSAAGAGCSKVLLTK 242
Cdd:PRK11181   69 GIIARVKPGR-QLQENDLpdllaSLEQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPK 128
rRNA_methyl_3 TIGR00186
rRNA methylase, putative, group 3; this is part of the trmH (spoU) family of rRNA methylases ...
 153-242 8.10e-05

rRNA methylase, putative, group 3; this is part of the trmH (spoU) family of rRNA methylases [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129290 [Multi-domain]  Cd Length: 237  Bit Score: 43.10  E-value: 8.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659569 153 KELPVDKLKGVSLIKVKfediKDWSDLVTPQGI-MGIFAKPDPVkMTYPETQLHH-----SLPLLLICDNLRDPGNLGTI 226
Cdd:TIGR00186  33 KLIQLAKKQGINIQLVD----RQKLDQLTKGGNhQGIAAKVKPI-LYKDLNDLYKtakskKQPFLLILDEITDPHNLGAI 107

                          90
                  ....*....|....*.
gi 1958659569 227 LRSAAGAGCSKVLLTK 242
Cdd:TIGR00186 108 LRTAEAFGVDGVILPK 123
 
Name Accession Description Interval E-value
SpoU COG0566
tRNA G18 (ribose-2'-O)-methylase SpoU [Translation, ribosomal structure and biogenesis]; tRNA ...
 112-249 4.79e-29

tRNA G18 (ribose-2'-O)-methylase SpoU [Translation, ribosomal structure and biogenesis]; tRNA G18 (ribose-2'-O)-methylase SpoU is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440332 [Multi-domain]  Cd Length: 265  Bit Score: 111.06  E-value: 4.79e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659569 112 KSRPFREKQGKILLEGRRLIADALKAGAVPKMFFFS-----RLEYIKELPvdKLKGVSLIKVKFEDIKDWSDLVTPQGIM 186
Cdd:COG0566    16 RDKKYREEEGLFLAEGRHAVEEALKAGREIEELLVTegaldRLAELLALA--KAAGIPVYEVSREVLDKLSGTETHQGVL 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958659569 187 GIFAKPDPVKMTYPETQLHHSlPLLLICDNLRDPGNLGTILRSAAGAGCSKVLLTKGCIYAYS 249
Cdd:COG0566    94 AVVRPPEYADLEDLLAEAGEP-PLLLVLDGVQDPGNLGAILRSAAAFGVDGVILPKRRADPYN 155
SpoU-like_RNMTL1 cd18106
SAM-dependent rRNA methylase related to RNMTL1; RNMTL1 (also known as HC90, MRM3 and RMTL1) ...
 210-245 3.19e-18

SAM-dependent rRNA methylase related to RNMTL1; RNMTL1 (also known as HC90, MRM3 and RMTL1) catalyzes the methylation of 2'-O-ribose residues G1370 to GmG residue of the mitochondrial 16S rRNA. RNMTL1 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349979  Cd Length: 148  Bit Score: 79.22  E-value: 3.19e-18
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958659569 210 LLLICDNLRDPGNLGTILRSAAGAGCSKVLLTKGCI 245
Cdd:cd18106     1 LTVICDNIRDPGNLGSILRSAAAAGCSKVLLTKGCV 36
SpoU-like_rRNA-MTase cd18095
SAM-dependent rRNA methylase related to SpoU-TrmH; RNA 2'-O ribose methyltransferase catalyzes ...
 210-254 3.70e-15

SAM-dependent rRNA methylase related to SpoU-TrmH; RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349968  Cd Length: 143  Bit Score: 70.53  E-value: 3.70e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1958659569 210 LLLICDNLRDPGNLGTILRSAAGAGCSKVLLTKGCIYAYSLLCMR 254
Cdd:cd18095     1 LVLVLDGVQDPGNLGTIIRTAAAFGVDGVILSKGTVDPYNPKVVR 45
SpoU_sub_bind smart00967
RNA 2'-O ribose methyltransferase substrate binding; This domain is a RNA 2'-O ribose ...
 125-191 2.71e-09

RNA 2'-O ribose methyltransferase substrate binding; This domain is a RNA 2'-O ribose methyltransferase substrate binding domain.


Pssm-ID: 214943 [Multi-domain]  Cd Length: 70  Bit Score: 52.54  E-value: 2.71e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659569  125 LEGRRLIADALKAGAVPKMFFFSRLEYIKELPVDKL---KGVSLIKVKFEDIKDWSDLVTPQGIMGIFAK 191
Cdd:smart00967   1 IEGRHAVEEALKSGRRIKELYLTEGRAERLKELLKLakeRGIKVIEVSKKELDKLSGTANHQGVVAVVKP 70
SpoU_methylase pfam00588
SpoU rRNA Methylase family; This family of proteins probably use S-AdoMet.
 209-249 9.92e-09

SpoU rRNA Methylase family; This family of proteins probably use S-AdoMet.


Pssm-ID: 425768  Cd Length: 142  Bit Score: 52.92  E-value: 9.92e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958659569 209 PLLLICDNLRDPGNLGTILRSAAGAGCSKVLLTK-GCIYAYS 249
Cdd:pfam00588   1 PLVVVLDNIQDPGNLGAIIRTAAAFGADGLILVEpRSADPYN 42
SpoU-like_RNA-MTase cd18104
SAM-dependent RNA methylase related to SpoU-TrmH; RNA 2'-O ribose methyltransferase catalyzes ...
 210-249 1.23e-08

SAM-dependent RNA methylase related to SpoU-TrmH; RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349977  Cd Length: 146  Bit Score: 52.58  E-value: 1.23e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1958659569 210 LLLICDNLRDPGNLGTILRSAAGAGCSKVLLTKGCIYAYS 249
Cdd:cd18104     1 LILVLEGLEKPGNLGAILRSADAAGADAVILCDPKTDLFN 40
SpoU-like_RNA-MTase cd18109
SAM-dependent RNA methylase related to SpoU-TrmH; RNA 2'-O ribose methyltransferase catalyzes ...
 210-249 1.46e-08

SAM-dependent RNA methylase related to SpoU-TrmH; RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349982  Cd Length: 141  Bit Score: 52.54  E-value: 1.46e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1958659569 210 LLLICDNLRDPGNLGTILRSAAGAGCSKVLLTKGCIYAYS 249
Cdd:cd18109     1 LTLALDGIQDPGNLGTIIRTADWFGIRQIICSPDTVDPYN 40
SpoU-like_RlmB cd18103
SAM-dependent rRNA methylase related to RlmB; 23S rRNA-M2G2251-MTase RlmB catalyzes the ...
 210-242 2.57e-07

SAM-dependent rRNA methylase related to RlmB; 23S rRNA-M2G2251-MTase RlmB catalyzes the methylation of guanosine 2251, a modification conserved in the peptidyltransferase domain of 23S rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349976  Cd Length: 143  Bit Score: 48.92  E-value: 2.57e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1958659569 210 LLLICDNLRDPGNLGTILRSAAGAGCSKVLLTK 242
Cdd:cd18103     1 LLLILDGITDPHNLGAIIRSAEAFGVDGVIIPK 33
SpoU-like_family cd18082
SAM-dependent rRNA or tRNA methylase related to SpoU; RNA 2'-O ribose methyltransferase ...
 212-245 5.94e-06

SAM-dependent rRNA or tRNA methylase related to SpoU; RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349955  Cd Length: 145  Bit Score: 44.91  E-value: 5.94e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1958659569 212 LICDNLRDPGNLGTILRSAAGAGCSKVLLTKGCI 245
Cdd:cd18082     2 LVLDNIRSPGNIGSIFRTADAFGVEKIYLVGPTA 35
SpoU-like cd18097
SAM-dependent rRNA or tRNA methylase related to SpoU; RNA 2'-O ribose methyltransferase ...
 210-241 7.04e-06

SAM-dependent rRNA or tRNA methylase related to SpoU; RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349970  Cd Length: 144  Bit Score: 44.86  E-value: 7.04e-06
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1958659569 210 LLLICDNLRDPGNLGTILRSAAGAGCSKVLLT 241
Cdd:cd18097     1 LVVVLDNLRSAHNVGSIFRTADAAGVEKIYLC 32
PRK11181 PRK11181
23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB;
187-242 8.43e-06

23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB;


Pssm-ID: 183021 [Multi-domain]  Cd Length: 244  Bit Score: 46.11  E-value: 8.43e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958659569 187 GIFAKPDPVKmTYPETQL-----HHSLPLLLICDNLRDPGNLGTILRSAAGAGCSKVLLTK 242
Cdd:PRK11181   69 GIIARVKPGR-QLQENDLpdllaSLEQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPK 128
rRNA_methyl_3 TIGR00186
rRNA methylase, putative, group 3; this is part of the trmH (spoU) family of rRNA methylases ...
 153-242 8.10e-05

rRNA methylase, putative, group 3; this is part of the trmH (spoU) family of rRNA methylases [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129290 [Multi-domain]  Cd Length: 237  Bit Score: 43.10  E-value: 8.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659569 153 KELPVDKLKGVSLIKVKfediKDWSDLVTPQGI-MGIFAKPDPVkMTYPETQLHH-----SLPLLLICDNLRDPGNLGTI 226
Cdd:TIGR00186  33 KLIQLAKKQGINIQLVD----RQKLDQLTKGGNhQGIAAKVKPI-LYKDLNDLYKtakskKQPFLLILDEITDPHNLGAI 107

                          90
                  ....*....|....*.
gi 1958659569 227 LRSAAGAGCSKVLLTK 242
Cdd:TIGR00186 108 LRTAEAFGVDGVILPK 123
SpoU-like_MRM1 cd18105
SAM-dependent rRNA methylase related to MRM1; MRM1 catalyzes the methylation of 2'-O-ribose ...
 210-242 3.19e-04

SAM-dependent rRNA methylase related to MRM1; MRM1 catalyzes the methylation of 2'-O-ribose residues G1145 to GmG residue of the mitochondrial 16S rRNA. MRM1 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349978  Cd Length: 158  Bit Score: 40.19  E-value: 3.19e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1958659569 210 LLLicDNLRDPGNLGTILRSAAGAGCSKVLLTK 242
Cdd:cd18105     3 LLL--DEITDPQNLGAILRSAYFLGVDGVVVSS 33
SpoU_sub_bind pfam08032
RNA 2'-O ribose methyltransferase substrate binding; This domain is a RNA 2'-O ribose ...
 124-192 4.52e-03

RNA 2'-O ribose methyltransferase substrate binding; This domain is a RNA 2'-O ribose methyltransferase substrate binding domain.


Pssm-ID: 429793 [Multi-domain]  Cd Length: 74  Bit Score: 35.29  E-value: 4.52e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958659569 124 LLEGRRLIADALKAGAVPKMFFFSRLEYIKEL-PVDKL---KGVSLIKVKFEDIKDWSDLVTPQGIMGIFAKP 192
Cdd:pfam08032   1 LIYGRHAVLEALKSGPEIKKLYLTEGRRDPRLkELLKLakeRGIKVEEVDRKKLDKLSGTANHQGVVAEVKPY 73
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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