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Catalytic Site Atlas

CSA LITERATURE entry for 1ze1

E.C. nametRNA pseudouridine55 synthase
SpeciesThermotoga maritima (Bacteria)
E.C. Number (IntEnz) 5.4.99.25
CSA Homologues of 1ze1There are 17 Homologs
CSA Entries With UniProtID Q9WZW0
CSA Entries With EC Number 5.4.99.25
PDBe Entry 1ze1
PDBSum Entry 1ze1
MACiE Entry M0056

Literature Report

IntroductiontRNA-pseudouridine synthase I from Thermotoga maritima catalyses the conversion of tRNA uridine to tRNA pseudouridine at position 55 in transfer RNA. The formation of pseudouridine is shown to be important for the structural integrity of transfer-RNA.
MechansimThere are two proposed mechanisms for this reaction. Based on references, the acyl-enzyme mechanism is shown rather than the Michael addition mechanism. 1. Asp 39 nucleophilically attacks the C1' atom of the ribose, detaching the uracil base from the ribose. 2. Rotation of the detached base occurs, and re-attachment of the rotated base results in the formation of the C5-C1' bond between the base and the ribose, and detaching Asp 39. 3. The OH group of Tyr 67 donates its proton to N1 atom of the base, while abstracting the C5 proton from the base.
Reaction

Catalytic Sites for 1ze1

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspA3939macie:sideChainActs as a nucleophile by attacking C1' of the scissile bond.
TyrA6767macie:sideChainThe negative pi-cloud of Tyr 67 stabilises the oxocarbenium intermediate. Tyr 67 also donates its proton to N1 of the base, while abstracting the C5 proton.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspB3939macie:sideChainActs as a nucleophile by attacking C1' of the scissile bond.
TyrB6767macie:sideChainThe negative pi-cloud of Tyr 67 stabilises the oxocarbenium intermediate. Tyr 67 also donates its proton to N1 of the base, while abstracting the C5 proton.

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspC3939macie:sideChainActs as a nucleophile by attacking C1' of the scissile bond.
TyrC6767macie:sideChainThe negative pi-cloud of Tyr 67 stabilises the oxocarbenium intermediate. Tyr 67 also donates its proton to N1 of the base, while abstracting the C5 proton.

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspD3939macie:sideChainActs as a nucleophile by attacking C1' of the scissile bond.
TyrD6767macie:sideChainThe negative pi-cloud of Tyr 67 stabilises the oxocarbenium intermediate. Tyr 67 also donates its proton to N1 of the base, while abstracting the C5 proton.

Literature References

Notes:
Phannachet K
Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase.
Biochemistry 2005 44 15488-15494
PubMed: 16300397
Mueller EG.
Chips off the old block.
Nat Struct Biol 2002 9 320-322
PubMed: 11976723
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