Top Level Name

  ⌊ Superfamily (core) Radical SAM

    ⌊ Subgroup methyltransferase (Class A)

     ⌊ Family adenosine C2 methyltransferase (RlmN-like)

  ⌊ FunctionalDomain RlmN-like sequence (ID 414329)

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 2002017 Taxon ID: 591020 281601919 ADA74903.1 (Genbank) URP

Uniprot

Protein NameAccessionEC Number Identifier
n/a D2AGW1 D2AGW1_SHIF2 (TrEMBL)

Sequence

Length of Enzyme (full-length): 340 | Length of Functional Domain: 329

1       10        20        30        40        50        60

MMKWMYHYCCDNFDEMTDINKVLRGKLKEVAEIRAPEVVEEQRSSDGTIKWAIAVGDQRV
ETVYIPEDDRATLCVSSQVGCALECKFCSTAQQGFNRNLRVSEIIGQVWRAAKIVGAAKV
TGQRPITNVVMMGMGEPLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKLGD
MIDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNANQGRVTIEYVMLDH
VNDGTEHAHQLAELLKDTPCKINLIPWNPFPDAPYGRSSNSRIDRFSKVLMSYGFTTIVR
KTRGDDIDAACGQLAGDVIDRTKRTLRKRMQGEAIDIKAV
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
81 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
85 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
88 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
74 Cys (C) side chain Nuceophile covalent catalysis -- reactant ISS
81 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
85 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
88 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ISS
311 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
61 Glu (E) side chain General Acid/Base proton relay -- reactant ICS PubMed:22097883
74 Cys (C) side chain Nucleophile, initiates reductive cleavage of S-S bond covalent catalysis -- reactant IDA PubMed:22097883
81 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ICS PubMed:22097883
85 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ICS PubMed:22097883
88 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding ICS PubMed:22097883
311 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
5HR6 X-Ray Crystal Structure Of C118A Rlmn With Cross-Linked Trna Purified From Escherichia Coli Rlmn Methylase • Trna Glu 24 2.88 S-Methylcysteine
(4 more ⇓) 		CSA • PDB • PDBSum
5HR7 X-Ray Crystal Structure Of C118A Rlmn From Escherichia Coli With Cross-Linked In Vitro Transcribed Trna Trna Glu • Dual-Specificity Rna Methyltransferase Rlmn 24 2.4 S-(Dimethylarsenic)Cysteine
(5 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
Oct. 16, 2014, 6:32 a.m. update curation agent holliday setDomainBoundaries.py
Dec. 17, 2015, 5:44 a.m. update curation agent setDomainBoundaries.py holliday
update family assignment evidence code IEA ISS
update name RlmN RlmN-like sequence
Jan. 18, 2016, 5:38 a.m. update curation agent holliday setDomainBoundaries.py
Oct. 15, 2016, 6:16 a.m. update domain end position 339 329
EC number assigned by UniProtKB accession ID.