RegulonDB RegulonDB 10.8: Gene Form
   

rlmD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

barA relA rlmD CRP HipB HipAB ppGpp TSS_3088 TSS_3088 rlmDp rlmDp TSS_3087 TSS_3087 relAp4 relAp4 relAp2 relAp2 relAp1 relAp1 relAp3 relAp3 TSS_3086 TSS_3086 TSS_3085 TSS_3085

Gene      
Name: rlmD    Texpresso search in the literature
Synonym(s): ECK2779, EG11247, b2785, rumA, ygcA
Genome position(nucleotides): 2913699 <-- 2915000 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.46
External database links:  
ASAP:
ABE-0009127
ECHOBASE:
EB1228
OU-MICROARRAY:
b2785
PortEco:
rlmD
STRING:
511145.b2785
COLOMBOS: rlmD


Product      
Name: 23S rRNA m5U1939 methyltransferase
Synonym(s): RlmD, RumA, YgcA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 48.052
Isoelectric point: 8.653
Motif(s):
 
Type Positions Sequence
10 -> 68 RTTTRQIITVSVNDLDSFGQGVARHNGKTLFIPGLLPQENAEVTVTEDKKQYARAKVVR
11 -> 67 TTTRQIITVSVNDLDSFGQGVARHNGKTLFIPGLLPQENAEVTVTEDKKQYARAKVV
2 -> 433 AQFYSAKRRTTTRQIITVSVNDLDSFGQGVARHNGKTLFIPGLLPQENAEVTVTEDKKQYARAKVVRRLSDSPERETPRCPHFGVCGGCQQQHASVDLQQRSKSAALARLMKHDVSEVIADVPWGYRRRARLSLNYLPKTQQLQMGFRKAGSSDIVDVKQCPILAPQLEALLPKVRACLGSLQAMRHLGHVELVQATSGTLMILRHTAPLSSADREKLERFSHSEGLDLYLAPDSEILETVSGEMPWYDSNGLRLTFSPRDFIQVNAGVNQKMVARALEWLDVQPEDRVLDLFCGMGNFTLPLATQAASVVGVEGVPALVEKGQQNARLNGLQNVTFYHENLEEDVTKQPWAKNGFDKVLLDPARAGAAGVMQQIIKLEPIRIVYVSCNPATLARDSEALLKAGYTIARLAMLDMFPHTGHLESMVLFSRVK
58 -> 63 KKQYAR
23 -> 40 DLDSFGQGVARHNGKTLF

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.3 - RNA modification
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0008168 - methyltransferase activity
GO:0016740 - transferase activity
GO:0046872 - metal ion binding
GO:0008173 - RNA methyltransferase activity
GO:0003723 - RNA binding
GO:0051536 - iron-sulfur cluster binding
GO:0051539 - 4 iron, 4 sulfur cluster binding
GO:0005506 - iron ion binding
GO:0070041 - rRNA (uridine-C5-)-methyltransferase activity
biological_process GO:0031167 - rRNA methylation
GO:0006396 - RNA processing
GO:0006364 - rRNA processing
GO:0032259 - methylation
GO:0070475 - rRNA base methylation
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-12119N
ECOCYC:
EG11247-MONOMER
ECOLIWIKI:
b2785
INTERPRO:
IPR001566
INTERPRO:
IPR030391
INTERPRO:
IPR030390
INTERPRO:
IPR029063
INTERPRO:
IPR012340
INTERPRO:
IPR010280
INTERPRO:
IPR002792
MODBASE:
P55135
PANTHER:
PTHR11061
PDB:
2BH2
PDB:
1UWV
PFAM:
PF05958
PFAM:
PF01938
PRIDE:
P55135
PRODB:
PRO_000023895
PROSITE:
PS01230
PROSITE:
PS01231
PROSITE:
PS50926
PROSITE:
PS51687
REFSEQ:
NP_417265
SMR:
P55135
UNIPROT:
P55135


Operon      
Name: rlmD         
Operon arrangement:
Transcription unit        Promoter
rlmD


Regulation by small RNA    
  Display Regulation
small RNA oxyS


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_3085 2913146 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3086 2913158 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3087 2915029 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3088 2916877 forward nd [RS-EPT-CBR] [1]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


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