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



Gene: rluC Accession Numbers: EG11118 (EcoCyc), b1086, ECK1071

Synonyms: yceC, ribosomal large subunit pseudouridine synthase C, ribosomal large subunit (23S rRNA) pseudouridine synthase C

Regulation Summary Diagram: ?

Summary:
RluC catalyzes pseudouridylation of nucleotides U955, U2504, and U2580 in 23S rRNA; all three sites are located near the peptidyl transferase center of the ribosome [Conrad98, Huang98d]. RluC also shows activity toward 16S rRNA in vitro [Huang98d].

RluC associates with a pre-50S ribosomal particle [Jiang07b]. A proteolytic fragment consisting of amino acids 89-319 is catalytically active [Corollo99]. The crystal structure of the C-terminal catalytic domain has been determined at 2 Å resolution [Mizutani04a].

An rluC mutant lacks pseudouridylation of nucleotides U955, U2504, and U2580 in 23S rRNA, but does not exhibit an obvious growth defect [Conrad98, Huang98d]. It was later shown that an rluC mutant shows some cold sensitivity [Jiang07b]. Insertion mutations in rluC suppress the cold-sensitive growth phenotype of a bipA deletion mutant [Krishnan08]. Inactivation of rluC leads to increased susceptibility to antibiotics that target the peptidyl transferase center, such as clindamycin, linezolid, and tiamulin [Toh08a].

Review: [Hamma06]

RluC: "ribosomal large subunit pseudouridine synthase C" [Conrad98]

Locations: cytosol

Map Position: [1,144,163 -> 1,145,122] (24.66 centisomes)
Length: 960 bp / 319 aa

Molecular Weight of Polypeptide: 36.027 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003675 , DIP:DIP-47832N , EchoBASE:EB1108 , EcoGene:EG11118 , EcoliWiki:b1086 , ModBase:P0AA39 , OU-Microarray:b1086 , PortEco:rluC , PR:PRO_000023778 , Pride:P0AA39 , Protein Model Portal:P0AA39 , RefSeq:NP_415604 , RegulonDB:EG11118 , SMR:P0AA39 , String:511145.b1086 , UniProt:P0AA39

Relationship Links: InterPro:IN-FAMILY:IPR002942 , InterPro:IN-FAMILY:IPR006145 , InterPro:IN-FAMILY:IPR006224 , InterPro:IN-FAMILY:IPR006225 , InterPro:IN-FAMILY:IPR020103 , PDB:Structure:1V9K , PDB:Structure:1XPI , Pfam:IN-FAMILY:PF00849 , Pfam:IN-FAMILY:PF01479 , Prosite:IN-FAMILY:PS01129 , Prosite:IN-FAMILY:PS50889 , Smart:IN-FAMILY:SM00363

In Paralogous Gene Group: 252 (4 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0000455 - enzyme-directed rRNA pseudouridine synthesis Inferred from experiment [Huang98d, Conrad98]
GO:0001522 - pseudouridine synthesis Inferred by computational analysis [GOA01]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0009982 - pseudouridine synthase activity Inferred from experiment Inferred by computational analysis [GOA01, Huang98d]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for rluC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Last-Curated ? 06-Oct-2008 by Keseler I , SRI International


Enzymatic reaction of: 23S rRNA pseudouridine synthase

EC Number: 5.4.99.24

uridine955/2504/2580 in 23S rRNA <=> a pseudouridine955/2504/2580 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 Citations Comment
Conserved-Region 20 -> 83
[UniProt09]
UniProt: S4 RNA-binding;
Active-Site 144
[UniProt10]
UniProt: Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b1086 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11118; 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

Conrad98: Conrad J, Sun D, Englund N, Ofengand J (1998). "The rluC gene of Escherichia coli codes for a pseudouridine synthase that is solely responsible for synthesis of pseudouridine at positions 955, 2504, and 2580 in 23 S ribosomal RNA." J Biol Chem 273(29);18562-6. PMID: 9660827

Corollo99: Corollo D, Blair-Johnson M, Conrad J, Fiedler T, Sun D, Wang L, Ofengand J, Fenna R (1999). "Crystallization and characterization of a fragment of pseudouridine synthase RluC from Escherichia coli." Acta Crystallogr D Biol Crystallogr 55 ( Pt 1);302-4. PMID: 10089432

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

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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

Huang98d: Huang L, Ku J, Pookanjanatavip M, Gu X, Wang D, Greene PJ, Santi DV (1998). "Identification of two Escherichia coli pseudouridine synthases that show multisite specificity for 23S RNA." Biochemistry 37(45);15951-7. PMID: 9843401

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

Jiang07b: 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

Krishnan08: Krishnan K, Flower AM (2008). "Suppression of {Delta}bipA Phenotypes in Escherichia coli by Abolishment of Pseudouridylation at Specific Sites on the 23S rRNA." J Bacteriol 190(23):7675-83. PMID: 18820021

Mizutani04a: Mizutani K, Machida Y, Unzai S, Park SY, Tame JR (2004). "Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli." Biochemistry 43(15);4454-63. PMID: 15078091

Toh08a: Toh SM, Mankin AS (2008). "An indigenous posttranscriptional modification in the ribosomal peptidyl transferase center confers resistance to an array of protein synthesis inhibitors." J Mol Biol 380(4);593-7. PMID: 18554609

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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 Wed Nov 26, 2014, biocyc13.