MetaCyc Enzyme: 16S rRNA pseudouridine 516 synthase

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

Synonyms: yejD

Species: Escherichia coli K-12 substr. MG1655

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 [Sivaraman02a].

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]

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

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 [GOA01a]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Butland05]
GO:0009982 - pseudouridine synthase activity Inferred from experiment Inferred by computational analysis [GOA01a, Wrzesinski95]
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, LopezCampistrou05]
GO:0005737 - cytoplasm

MultiFun Terms: information transfer RNA related RNA modification

Imported from EcoCyc 02-Jun-2015 by Paley S , 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.

Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

Sequence Features

Feature Class Location Common Name Citations Comment
Conserved-Region 1 -> 68  
UniProt: S4 RNA-binding;
Mutagenesis-Variant 102  
[Conrad99, UniProt11]
N or T: Loss of activity.
Active-Site 102 catalytic aspartate residue

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


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

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

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

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

Sivaraman02a: 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.

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."

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 MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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