RegulonDB RegulonDB 11.2: Gene Form
   

rluD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rluD bamD yfiH ryfD clpB RybB TSS_2929 TSS_2929 TSS_2928 TSS_2928 TSS_2927 TSS_2927 TSS_2926 TSS_2926 TSS_2925 TSS_2925 TSS_2924 TSS_2924 TSS_2923 TSS_2923 TSS_2922 TSS_2922 TSS_2921 (cluster) TSS_2921 (cluster) TSS_2920 (cluster) TSS_2920 (cluster) TSS_2919 TSS_2919 TSS_2918 TSS_2918 TSS_2917 TSS_2917 TSS_2916 (cluster) TSS_2916 (cluster) TSS_2915 TSS_2915 bamDp1 bamDp1 bamDp2 bamDp2 TSS_2914 TSS_2914 TSS_2913 TSS_2913 TSS_2912 TSS_2912 TSS_2911 TSS_2911 TSS_2910 TSS_2910 TSS_2909 TSS_2909 ryfDp ryfDp TSS_2908 (cluster) TSS_2908 (cluster) TSS_2907 TSS_2907 clpBp2 clpBp2 clpBp clpBp TSS_2905 TSS_2905 TSS_2904 (cluster) TSS_2904 (cluster)

Gene      
Name: rluD    Texpresso search in the literature
Synonym(s): ECK2592, EG12098, b2594, sfhB, yfiI
Genome position(nucleotides): 2735031 <-- 2736011
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.8
External database links:  
ASAP:
 ABE-0008532
ECHOBASE:
 EB2022
ECOLIHUB:
 rluD
OU-MICROARRAY:
 b2594
STRING:
 511145.b2594
COLOMBOS: rluD


Product      
Name: 23S rRNA pseudouridine1911/1915/1917 synthase
Synonym(s): RluD, SfhB, YfiI
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 37.122
Isoelectric point: 6.81
Motif(s):
 
Type Positions Sequence Comment
2 -> 326 AQRVQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEHKDEVDWL UniProt: Ribosomal large subunit pseudouridine synthase D.
18 -> 65 QRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQV
92 -> 242 DIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAH
139 -> 139 D UniProt: Loss of activity..
271 -> 326 LRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEHKDEVDWL UniProt: In Ref. 2..

 
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:0120159 - rRNA pseudouridine synthase activity
GO:0005515 - protein binding
GO:0016853 - isomerase activity
GO:0003723 - RNA binding
GO:0009982 - pseudouridine synthase activity
biological_process GO:0009451 - RNA modification
GO:0000027 - ribosomal large subunit assembly
GO:0001522 - pseudouridine synthesis
GO:0006364 - rRNA processing
GO:0000455 - enzyme-directed rRNA pseudouridine synthesis
Note(s): Note(s): ...[more].
Reference(s): [1] Gustafsson C., et al., 1996
[2] Leppik M., et al., 2017
[3] Lescat M., et al., 2017
External database links:  
ALPHAFOLD:
 P33643
DIP:
 DIP-10721N
ECOCYC:
 EG12098-MONOMER
ECOLIWIKI:
 b2594
INTERPRO:
 IPR006145
INTERPRO:
 IPR006224
INTERPRO:
 IPR002942
INTERPRO:
 IPR006225
INTERPRO:
 IPR020103
INTERPRO:
 IPR036986
MODBASE:
 P33643
PDB:
 1QYU
PDB:
 1PRZ
PDB:
 1V9F
PDB:
 2IST
PFAM:
 PF00849
PFAM:
 PF01479
PRIDE:
 P33643
PRODB:
 PRO_000023779
PROSITE:
 PS50889
PROSITE:
 PS01129
REFSEQ:
 NP_417085
SMART:
 SM00363
SMR:
 P33643
UNIPROT:
 P33643


Operon      
Name: rluD-yfiH         
Operon arrangement:
Transcription unit        Promoter
rluD-pgeF


Regulation by small RNA    
  Display Regulation
small RNA rybB


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_2904 (cluster) 2734197 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2905 2734202 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2907 2734207 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2908 (cluster) 2734293 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2909 2735050 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2910 2735058 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2911 2735067 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2912 2735835 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2913 2735898 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_2914 2735960 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2915 2736025 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2916 (cluster) 2736071 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2917 2736085 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2918 2736248 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2919 2736286 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2920 (cluster) 2736329 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2921 (cluster) 2736345 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2922 2736549 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2923 2736555 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2924 2736559 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2925 2736561 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2926 2736565 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2927 2736586 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2928 2736612 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2929 2736658 reverse nd [RS-EPT-CBR] [4]


Evidence    

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


Reference(s)    

 [1] Gustafsson C., Reid R., Greene PJ., Santi DV., 1996, Identification of new RNA modifying enzymes by iterative genome search using known modifying enzymes as probes., Nucleic Acids Res 24(19):3756-62

 [2] Leppik M., Liiv A., Remme J., 2017, Random pseuoduridylation in vivo reveals critical region of Escherichia coli 23S rRNA for ribosome assembly., Nucleic Acids Res 45(10):6098-6108

 [3] Lescat M., Launay A., Ghalayini M., Magnan M., Glodt J., Pintard C., Dion S., Denamur E., Tenaillon O., 2017, Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut., Mol Ecol 26(7):1802-1817

 [4] 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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