Get   for     ? 
 Site search     ? 
Catalytic Site Atlas Version 2.2.12
Find Annotated Site: PDB code:
Swiss-Prot code:
EC number:
Help
CSA entry for 1ze1
Original Entry
Title:
Lyase
Compound:
Trna pseudouridine synthase b
Mutant:
No
UniProt/Swiss-Prot:
Q9WZW0-TRUB_THEMA
EC Class:
4.2.1.70
Other CSA Entries:
Overview of all sites for 1ze1
Homologues of 1ze1
Entries for UniProt/Swiss-Prot: Q9WZW0
Entries for EC: 4.2.1.70
Other Databases:
PDB entry: 1ze1
PDBsum entry: 1ze1
UniProt/Swiss-Prot: Q9WZW0
IntEnz entry: 4.2.1.70
Literature Report:
Introduction:
tRNA-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.
Mechanism:
There 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.
Sites:

Click to Display Catalytic Site (Get help with this section)
Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 39 39Sidechain
NucleophileSubstrate
Acts as a nucleophile by attacking C1' of the scissile bond.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11976723 Current protein Conservation of residue
PubMed ID 11976723 Current protein Mutagenesis of residue
PubMed ID 16300397 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
TYRA 67 67Sidechain
ElectrostaticSubstrate
Acid/baseSubstrate
The 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.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11976723 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 16300397 Current protein Mutagenesis of residue
PubMed ID 16300397 Current protein Conservation of residue
Notes:

References:
1
Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase.
K. Phannachet and Y. Elias and R. H. Huang
Biochemistry 44, (47) 15488-94, (2005).
16300397
2
Chips off the old block.
E. G. Mueller
Nat Struct Biol 9, (5) 320-2, (2002).
11976723
Which EBI biological databases are available and how do I access them? EBI Site Map