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: ?

Regulation summary diagram for rluB

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 [Jiang07a]. 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 [Czudnochowski14].

The conserved active site residue Asp110 is essential for activity [Del01], while a Tyr140Phe mutant retains 3% of wild-type enzymatic activity [Czudnochowski14]. 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 [Jiang07a].

Review: [Hamma06]

Locations: cytosol

Map Position: [1,324,876 -> 1,325,751] (28.56 centisomes, 103°)
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: ?

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 [GOA01a]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05]
GO:0009982 - pseudouridine synthase activity Inferred from experiment Inferred by computational analysis [GOA01a, Del01]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016866 - intramolecular transferase activity Inferred by computational analysis [GOA01a]
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]

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

Enzymatic reaction of: 23S rRNA pseudouridine 2605 synthase

EC Number:

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

Protein sequence of 23S rRNA pseudouridine 2605 synthase with features indicated

Feature Class Location Common Name Citations Comment
Conserved-Region 3 -> 75  
UniProt: S4 RNA-binding;
Mutagenesis-Variant 110  
[Del01, UniProt11]
D → N or T: Loss of activity.
Active-Site 110 active site aspartate residue

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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


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

Czudnochowski14: Czudnochowski N, Ashley GW, Santi DV, Alian A, Finer-Moore J, Stroud RM (2014). "The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs." Nucleic Acids Res 42(3);2037-48. 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

GOA01a: 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

Jiang07a: 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.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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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 19.0 on Thu Oct 8, 2015, BIOCYC14A.