UniProt Accession

 RLMD_ECOLI; P55135; Q2MA47 

Genbank Protein ID

 U29580; U00096; AP009048 

Genbank Nucleotide ID

 AAA69295.1; AAC75827.1; BAE76859.1 

Protein Name

 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD 

Protein Synonyms/Alias

 23S rRNA(m5U1939)-methyltransferase 

Gene Name

 rlmD 

Gene Synonyms/Alias

 rumA; ygcA; b2785; JW2756 

Created Date

 July 27, 2013 

Organism

 Escherichia coli (strain K12) 

NCBI Taxa ID

 83333 

Lysine Modification

Position	Peptide	Type	References
58	EVTVTEDKKQYARAK	acetylation	[1]
140	LSLNYLPKTQQLQMG	acetylation	[1]
349	NLEEDVTKQPWAKNG	acetylation	[1]
378	GVMQQIIKLEPIRIV	acetylation	[1]

Reference

 [1] Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli.
 Weinert BT, Iesmantavicius V, Wagner SA, Schölz C, Gummesson B, Beli P, Nyström T, Choudhary C.
 Mol Cell. 2013 Jul 25;51(2):265-72. [PMID: 23830618] 

Functional Description

 Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA. 

Sequence Annotation

 DOMAIN 10 68 TRAM.
 REGION 23 40 Interaction with RNA.
 REGION 58 63 Interaction with RNA.
 ACT_SITE 389 389 Nucleophile.
 METAL 81 81 Iron-sulfur (4Fe-4S).
 METAL 87 87 Iron-sulfur (4Fe-4S).
 METAL 90 90 Iron-sulfur (4Fe-4S).
 METAL 162 162 Iron-sulfur (4Fe-4S).
 BINDING 265 265 S-adenosyl-L-methionine.
 BINDING 294 294 S-adenosyl-L-methionine; via carbonyl
 BINDING 299 299 S-adenosyl-L-methionine.
 BINDING 315 315 S-adenosyl-L-methionine.
 BINDING 342 342 S-adenosyl-L-methionine.
 BINDING 363 363 S-adenosyl-L-methionine.  

Keyword

 3D-structure; 4Fe-4S; Complete proteome; Direct protein sequencing; Iron; Iron-sulfur; Metal-binding; Methyltransferase; Reference proteome; rRNA processing; S-adenosyl-L-methionine; Transferase. 

Sequence Source

 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 

Protein Length

 433 AA 

Protein Sequence

Gene Ontology

 GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoCyc.
 GO:0005506; F:iron ion binding; IEA:HAMAP.
 GO:0003723; F:RNA binding; IEA:InterPro.
 GO:0070041; F:rRNA (uridine-C5-)-methyltransferase activity; IDA:EcoCyc.
 GO:0070475; P:rRNA base methylation; IDA:EcoCyc. 

Interpro

 IPR001566; 23S_rRNA_MeTrfase_RlmD.
 IPR012340; NA-bd_OB-fold.
 IPR002792; TRAM_dom.
 IPR010280; U5_MeTrfase. 

Pfam

 PF01938; TRAM
 PF05958; tRNA_U5-meth_tr 

SMART

  

PROSITE

 PS50926; TRAM
 PS01230; TRMA_1
 PS01231; TRMA_2 

PRINTS