Top Level Name

  ⌊ Superfamily (core) Radical SAM

    ⌊ Subgroup methyltransferase (Class A)

     ⌊ Family adenosine C2 methyltransferase (RlmN-like)

  ⌊ FunctionalDomain RlmN-like sequence (ID 380584)

Superfamily Assignment Evidence Code(s) ISS
Family Assignment Evidence Code ISS
This entry was last updated onJune 10, 2017

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Shigella flexneri 2a str. 301 Taxon ID: 198214 24113846 NP_708356.1 (RefSeq)
Shigella flexneri Taxon ID: 623 445925473 WP_000003328.1 (RefSeq) URP
Shigella flexneri G1663 Taxon ID: 1435046 828442605 AKK55087.1 (Genbank) URP
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Uniprot

Protein NameAccessionEC Number Identifier
Dual-specificity RNA methyltransferase RlmN {ECO:0000255|HAMAP-Rule:MF_01849} Q0T202 RLMN_SHIF8 (Swiss-Prot)
Dual-specificity RNA methyltransferase RlmN {ECO:0000255|HAMAP-Rule:MF_01849} Q83K42 RLMN_SHIFL (Swiss-Prot)

Sequence

Length of Enzyme (full-length): 384 | Length of Functional Domain: 365

1       10        20        30        40        50        60

MSEQLVTPENVTTKDGKINLLDLNRQQMREFFKDLGEKTFRADQVMKWMYHYCCDNFDEM
TDINKVLRGKLKEVAEIRAPEVVEEQRSSDGTIKWAIAVGDQRVETVYIPEDDRATLCVS
SQVGCALECKFCSTAQQGFNRNLRVSEIIGQVWRAAKIVGAAKVTGQRPITNVVMMGMGE
PLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHAPNDE
IRDEIVPINKKYNIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLK
DTPCKINLIPWNPFPDAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDAACGQLAG
DVIDRTKRTLRKRMQGEAIDIKAV
This shows the full-length sequence of the enzyme. The region of the functional domain is highlighted in black letters, while the residual residues are shown in grey. The Superfamily domain, when present, is shown using underlining. In many cases the functional domain is the full-length sequence.
Conserved catalytic residues (as determined by automated alignment to family, subgroup, or superfamily HMMs) are shown with teal highlighting . Conserved catalytic residues which do not matched the Conserved Alignment Residue are shown with maroon highlighting . Information regarding their function can be found in the Conserved Residues section below.
FASTA formatted full-length sequence.
BLAST this sequence against SFLD.
Scan SFLD-HMMs with this sequence.

Conserved Residues
Superfamily CAR This EFD conserves 3/3 Superfamily-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
125 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
129 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
132 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
Subgroup CAR This EFD conserves 5/5 Subgroup-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
118 Cys (C) side chain Nuceophile covalent catalysis -- reactant ISS
125 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
129 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
132 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
355 Cys (C) side chain Nucleophile, Methyl donor covalent catalysis -- reactant ISS
Family CAR This EFD conserves 6/6 Family-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
105 Glu (E) side chain General Acid/Base proton relay -- reactant ICS PubMed:22097883
118 Cys (C) side chain Nucleophile, initiates reductive cleavage of S-S bond covalent catalysis -- reactant IDA PubMed:22097883
125 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ICS PubMed:22097883
129 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ICS PubMed:22097883
132 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ICS PubMed:22097883
355 Cys (C) side chain Nucleophile, forms methylthioether with methyl group from SAM covalent catalysis -- reactant IDA PubMed:22097883

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
3RF9 X-Ray Structure Of Rlmn From Escherichia Coli Ribosomal Rna Large Subunit Methyltransferase N 119 2.2 Iron/Sulfur Cluster • (4R)-2-Methylpentane-2,4-Diol CSA • PDB • PDBSum
3RFA X-Ray Structure Of Rlmn From Escherichia Coli In Complex With S-Adenosylmethionine Ribosomal Rna Large Subunit Methyltransferase N 118 2.05 S-Methylcysteine
(2 more ⇓) 		CSA • PDB • PDBSum
4PL2 X-Ray Crystal Structure Of C118A Rlmn From Escherichia Coli Dual-Specificity Rna Methyltransferase Rlmn 143 2.2 Yes Iron/Sulfur Cluster CSA • PDB • PDBSum
4PL1 X-Ray Crystal Structure Of C118A Rlmn From Escherichia Coli With S-Adenosylmethionine Dual-Specificity Rna Methyltransferase Rlmn 139 2.58 Yes S-Methylcysteine
(2 more ⇓) 		CSA • PDB • PDBSum
Percent identity and alignment length from the BLAST match of the Functional Domain sequence to the PDB sequence.
"Yes" indicates that a GI associated with this Functional Domain was mapped to the PDB ID via UniProtKB.

Curation History
Time Change Annotation Old Value New Value
May 14, 2014, 3:30 a.m. update curation agent holliday setDomainBoundaries.py
update domain end position 384 383
Dec. 17, 2015, 5 a.m. update curation agent setDomainBoundaries.py holliday
update name uncharacterized Radical SAM superfamily sequence RlmN-like sequence
Jan. 18, 2016, 4:52 a.m. update curation agent holliday setDomainBoundaries.py
Oct. 15, 2016, 5:09 a.m. update domain end position 383 373
update domain start position 1 9
EC number assigned by UniProtKB accession ID.