Escherichia coli K-12 substr. MG1655 Enzyme: 16S rRNA pseudouridine 516 synthase

Gene: rsuA Accession Numbers: EG12044 (EcoCyc), b2183, ECK2177

Synonyms: yejD

Regulation Summary Diagram: ?

Regulation summary diagram for rsuA

RsuA is the pseudouridine synthase that is responsible for pseudouridylation of 16S rRNA at position 516 [Wrzesinski95, Conrad99]. In vitro, the enzyme does not modify free 16S rRNA. The preferred substrate is a 5'-terminal fragment of 16S rRNA complexed with 30S ribosomal proteins, suggesting that pseudouridylation occurs at an intermediate stage of 30S assembly in vivo [Wrzesinski95].

Crystal structures of RsuA in complex with uracil or UMP have been solved. Despite limited sequence similarity, the structure of RsuA is similar to that of TruA, a tRNA pseudouridine synthase [Sivaraman02].

An rsuA mutation causes a defect in pseudouridylation at position 516 in the 16S rRNA, and a D102N or D102T mutation at a conserved aspartate was shown to cause a defect in catalytic activity [Conrad99]. An rsuA mutant does not exhibit any obvious growth defect [Conrad99].

Reviews: [Hamma06, Hur06]

Locations: cytosol

Map Position: [2,277,810 <- 2,278,505] (49.09 centisomes, 177°)
Length: 696 bp / 231 aa

Molecular Weight of Polypeptide: 25.865 kD (from nucleotide sequence), 32.5 kD (experimental) [Wrzesinski95 ]

Unification Links: ASAP:ABE-0007223 , CGSC:36034 , DIP:DIP-35902N , EchoBASE:EB1978 , EcoGene:EG12044 , EcoliWiki:b2183 , Mint:MINT-1221744 , ModBase:P0AA43 , OU-Microarray:b2183 , PortEco:rsuA , PR:PRO_000023891 , Pride:P0AA43 , Protein Model Portal:P0AA43 , RefSeq:NP_416688 , RegulonDB:EG12044 , SMR:P0AA43 , String:511145.b2183 , UniProt:P0AA43

Relationship Links: InterPro:IN-FAMILY:IPR000748 , InterPro:IN-FAMILY:IPR002942 , InterPro:IN-FAMILY:IPR006145 , InterPro:IN-FAMILY:IPR018496 , InterPro:IN-FAMILY:IPR020103 , PDB:Structure:1KSK , PDB:Structure:1KSL , PDB:Structure:1KSV , 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 [Conrad99]
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 [Butland05]
GO:0009982 - pseudouridine synthase activity Inferred from experiment Inferred by computational analysis [GOA01, Wrzesinski95]
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, LopezCampistrou05]
GO:0005737 - cytoplasm

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for rsuA 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]

Last-Curated ? 30-Sep-2008 by Keseler I , SRI International

Enzymatic reaction of: 16S rRNA pseudouridine synthase (16S rRNA pseudouridine 516 synthase)

EC Number:

a uridine516 in 16S rRNA <=> a 16S rRNA pseudouridine516

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 16S rRNA pseudouridine 516 synthase with features indicated

Feature Class Location Common Name Citations Comment
Conserved-Region 1 -> 68  
UniProt: S4 RNA-binding;
Mutagenesis-Variant 102  
[Conrad99, UniProt11a]
D → N or T: Loss of activity.
Active-Site 102 catalytic aspartate residue
[Sivaraman02, Conrad99]

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b2183 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12044; 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

Conrad99: Conrad J, Niu L, Rudd K, Lane BG, Ofengand J (1999). "16S ribosomal RNA pseudouridine synthase RsuA of Escherichia coli: deletion, mutation of the conserved Asp102 residue, and sequence comparison among all other pseudouridine synthases." RNA 5(6);751-63. PMID: 10376875

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

Hur06: Hur S, Stroud RM, Finer-Moore J (2006). "Substrate recognition by RNA 5-methyluridine methyltransferases and pseudouridine synthases: a structural perspective." J Biol Chem 281(51);38969-73. PMID: 17085441

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

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

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Sivaraman02: Sivaraman J, Sauve V, Larocque R, Stura EA, Schrag JD, Cygler M, Matte A (2002). "Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP." Nat Struct Biol 9(5);353-8. PMID: 11953756

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."

Wrzesinski95: Wrzesinski J, Bakin A, Nurse K, Lane BG, Ofengand J (1995). "Purification, cloning, and properties of the 16S RNA pseudouridine 516 synthase from Escherichia coli." Biochemistry 34(27);8904-13. PMID: 7612632

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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