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Escherichia coli K-12 substr. MG1655 Enzyme: 23S rRNA pseudouridine 2605 synthase



Gene: rluB Accession Numbers: EG12433 (EcoCyc), b1269, ECK1263

Synonyms: yciL, ribosomal large subunit pseudouridine synthase B

Regulation Summary Diagram: ?

Summary:
RluB is the pseudouridine synthase that catalyzes formation of pseudouridine at position 2605 in 23S rRNA. RluB belongs to the RsuA family of RNA pseudouridine synthases [Del01].

RluB is associated with a particle the migrates slightly slower than the 50S ribosomal subunit, suggesting that it acts during 50S subunit maturation [Jiang07c]. Pseudouridine residues outside of helix-loop 69, including Ψ2605, appear to be made during the early steps of large ribosome subunit assembly [Siibak10, Chen13c].

Crystal structures of the catalytic domain alone and in a complex with the substrate stem-loop have been solved, revealing a covalent bond between the hydroxyl group of the active site Tyr140 and the C6 of the U2605 substrate with the base flipped into the active site. The authors propose a Michael addition reaction mechanism for pseudouridine synthesis [Czudnochowski13].

The conserved active site residue Asp110 is essential for activity [Del01], while a Tyr140Phe mutant retains 3% of wild-type enzymatic activity [Czudnochowski13]. An rluB null mutant or an rluB rluF double null mutant exhibits no obvious growth defect [Del01]. Deletion of rluB leads to accumulation of free 30S and 50S ribosomal subunits [Jiang07c].

Review: [Hamma06]

Locations: cytosol

Map Position: [1,324,876 -> 1,325,751] (28.56 centisomes)
Length: 876 bp / 291 aa

Molecular Weight of Polypeptide: 32.711 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004259 , DIP:DIP-11585N , EchoBASE:EB2329 , EcoGene:EG12433 , EcoliWiki:b1269 , ModBase:P37765 , OU-Microarray:b1269 , PortEco:rluB , PR:PRO_000023777 , Pride:P37765 , Protein Model Portal:P37765 , RefSeq:NP_415785 , RegulonDB:EG12433 , SMR:P37765 , String:511145.b1269 , UniProt:P37765

Relationship Links: InterPro:IN-FAMILY:IPR000748 , InterPro:IN-FAMILY:IPR002942 , InterPro:IN-FAMILY:IPR006145 , InterPro:IN-FAMILY:IPR018496 , InterPro:IN-FAMILY:IPR020103 , PDB:Structure:4LAB , PDB:Structure:4LGT , Pfam:IN-FAMILY:PF00849 , Pfam:IN-FAMILY:PF01479 , Prosite:IN-FAMILY:PS01149 , Prosite:IN-FAMILY:PS50889 , Smart:IN-FAMILY:SM00363

In Paralogous Gene Group: 269 (4 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0000455 - enzyme-directed rRNA pseudouridine synthesis Inferred from experiment [Del01]
GO:0001522 - pseudouridine synthesis Inferred by computational analysis [GOA01]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05]
GO:0009982 - pseudouridine synthase activity Inferred from experiment Inferred by computational analysis [GOA01, Del01]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11]
GO:0016866 - intramolecular transferase activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for rluB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Credits:
Last-Curated ? 21-Nov-2013 by Keseler I , SRI International


Enzymatic reaction of: 23S rRNA pseudouridine 2605 synthase

EC Number: 5.4.99.22

uridine2605 in 23S rRNA <=> a pseudouridine2605 in 23S rRNA

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.


Sequence Features

Feature Class Location Common Name Citations Comment
Conserved-Region 3 -> 75  
[UniProt09]
UniProt: S4 RNA-binding;
Mutagenesis-Variant 110  
[Del01, UniProt11a]
Alternate sequence: D → T; UniProt: Loss of activity.
Alternate sequence: D → N; UniProt: Loss of activity.
Active-Site 110 active site aspartate residue
[Del01]
 


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b1269 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12433; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

Chen13c: Chen SS, Williamson JR (2013). "Characterization of the ribosome biogenesis landscape in E. coli using quantitative mass spectrometry." J Mol Biol 425(4);767-79. PMID: 23228329

Czudnochowski13: Czudnochowski N, Ashley GW, Santi DV, Alian A, Finer-Moore J, Stroud RM (2013). "The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs." Nucleic Acids Res. PMID: 24214967

Del01: Del Campo M, Kaya Y, Ofengand J (2001). "Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli." RNA 7(11);1603-15. PMID: 11720289

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Hamma06: Hamma T, Ferre-D'Amare AR (2006). "Pseudouridine synthases." Chem Biol 13(11);1125-35. PMID: 17113994

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Jiang07c: Jiang M, Sullivan SM, Walker AK, Strahler JR, Andrews PC, Maddock JR (2007). "Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques." J Bacteriol 189(9);3434-44. PMID: 17337586

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Siibak10: Siibak T, Remme J (2010). "Subribosomal particle analysis reveals the stages of bacterial ribosome assembly at which rRNA nucleotides are modified." RNA 16(10);2023-32. PMID: 20719918

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Thu Nov 27, 2014, biocyc11.