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Catalytic Site Atlas

CSA LITERATURE entry for 1dj0

E.C. nametRNA pseudouridine38-40 synthase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz)
CSA Homologues of 1dj01vs3,2nqp,2nr0,2nre,
CSA Entries With UniProtID P07649
CSA Entries With EC Number
PDBe Entry 1dj0
PDBSum Entry 1dj0
MACiE Entry 1dj0

Literature Report

IntroductionPseudouridylate synthase is a member of the pseudouridine synthase family and catalyses the synthesis of pseudourine, the C5-C1' isomer of uridine, in a variety of RNAs. Pseudouridine synthases display varying degrees of specificity for their individual, three dimensionally folded RNA substrates which include tRNA, rRNA and snRNA. Pseudouridine is the most abundant modified nucleoside in the cell and many of the sites targeted for pseudouridine formation, such as those that map to the peptidyl-transfer region of rRNA, are highly conserved in evolution.
MechansimThe minimal chemical mechanism for this reaction involves three steps: (i) cleavage of the N-glycosidic linkage of the target uridine (ii) rotation of the uracil ring to position C5 of the pyrimidine near C1' of the ribosyl group of the RNA and (iii) formation of a new C1'-C5 carbon-carbon bond. Asp60 is thought to be catalytic base and is positioned to carry out a nucleophilic attack by electrostatic shielding caused by Arg58 and Arg205 binding specific phosphate groups of the tRNA.

Catalytic Sites for 1dj0

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription

Literature References

Mueller EG.
Chips off the old block.
Nat Struct Biol 2002 9 320-322
PubMed: 11976723
Ferré-D'Amaré AR.
RNA-modifying enzymes.
Curr Opin Struct Biol 2003 13 49-55
PubMed: 12581659
Johnson J
Intraobserver and interobserver agreement of the interpretation of pediatric chest radiographs.
Emerg Radiol 2010 17 285-290
PubMed: 20091078