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Overview for MACiE Entry M0056

Version history

General Information

EC Number: 5.4.99.12 (A member of the Isomerases, Intramolecular transferases, Transferring other groups)

Enzyme Name: tRNA-pseudouridine synthase I

Biological Species: Thermotoga maritima (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • Q9WZW0 - tRNA pseudouridine synthase B

Representative PDB Code: 1ze1 - CONFORMATIONAL CHANGE OF PSEUDOURIDINE 55 SYNTHASE UPON ITSASSOCIATION WITH RNA SUBSTRATE (Resolution = 2.90 Å).

Catalytic CATH Codes:

  • Unassigned Domain

Display structure information

Overall Reaction:

Image of tRNA uridine

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Image of tRNA pseudouridine

tRNA uridine
C00868
tRNA pseudouridine
C02764

Overall Comment: There are two commonly proposed mechanisms for this enzyme. Based on references 2 and 3 we show the acyl-enzyme mechanism rather than the alternative Michael addition mechanism.


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Stepwise Description of the Reaction

Step 1Asp39 initiates a nucleophilic attack upon the C1 of the uridine tRNA in a substitution reaction, displacing the uridine base as an anion.
Step 2The uridine undergoes rotation within the active site. The anion then initiates double bond rearrangement, which results in nucleophilic attack of the transient carbanion (from the C=C) on the covalently bound tRNA molecule in a substitution reaction, displacing Asp39.
Step 3The pseudouridine then deprotonates Tyr67, which in turn deprotonates the sugar bound carbon of the ring forming the final product.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Asp 39 A Side Chain
Tyr 67 A Side Chain

References

  1. P. G. Foster et al. (2000), Nat. Struct. Biol., 7, 23-27. The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I.
    Medline: 10625422
  2. E. G. Mueller (2002), Nat. Struct. Biol., 9, 320-322. Chips off the old block.
    Medline: 11976723
  3. K. Phannachet et al. (2005), Biochemistry, 44, 15488-15494. Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase.
    Medline: 16300397

Homologue information for M0056 (1ze1)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

GOA logo
pseudouridine synthesis (biological process)
RNA binding (molecular function)
RNA processing (biological process)
tRNA processing (biological process)
RNA modification (biological process)
pseudouridine synthase activity (molecular function)
isomerase activity (molecular function)
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