PDBsum entry 2ab4

Isomerase/RNA

PDB id: 2ab4

Contents

Protein chain

300 a.a. *

DNA/RNA

Metals

_ZN

Waters ×82

* Residue conservation analysis

PDB id:

2ab4

Name:

Isomerase/RNA

Title:

Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase

Structure:

5'-r( Cp Cp Ap Cp Gp Gp Up (Fhu) p Cp Gp Ap Ap Up Cp Cp Gp Up Gp Gp C)-3'. Chain: b. Engineered: yes. tRNA pseudouridine synthase b. Chain: a. Synonym: tRNA pseudouridine 55 synthase, psi55 synthase, tRNA-uridine isomerase, tRNA pseudouridylate synthase. Engineered: yes.

Source:

Synthetic: yes. Thermotoga maritima. Organism_taxid: 2336. Gene: trub. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.40Å R-factor: 0.222 R-free: 0.272

Authors:

K.Phannachet,Y.Elias,R.H.Huang

Key ref:

K.Phannachet et al. (2005). Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase. Biochemistry, 44, 15488-15494. PubMed id: 16300397 DOI: 10.1021/bi050961w

Date:

14-Jul-05 Release date: 13-Dec-05

Protein chain

Q9WZW0  (TRUB_THEMA) -  tRNA pseudouridine synthase B from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 309 a.a.

Struc: 300 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chain

C-C-A-C-G-G-U-FHU-C-G-A-A-U-C-C-G-U-G-G-C 20 bases

Enzyme reactions

• Enzyme class: E.C.5.4.99.25 - tRNA pseudouridine(55) synthase.
• Reaction: uridine₅₅ in tRNA = pseudouridine₅₅ in tRNA

DOI no: 10.1021/bi050961w

Biochemistry 44:15488-15494 (2005)

PubMed id: 16300397

Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase.

K.Phannachet, Y.Elias, R.H.Huang.

ABSTRACT

Sequence alignment of the TruA, TruB, RsuA, and RluA families of pseudouridine synthases (PsiS) identifies a strictly conserved aspartic acid, which has been shown to be the critical nucleophile for the PsiS-catalyzed formation of pseudouridine (Psi). However, superposition of the representative structures from these four families of enzymes identifies two additional amino acids, a lysine or an arginine (K/R) and a tyrosine (Y), from a K/RxY motif that are structurally conserved in the active site. We have created a series of Thermotoga maritima and Escherichia coli pseudouridine 55 synthase (Psi55S) mutants in which the conserved Y is mutated to other amino acids. A new crystal structure of the T. maritima Psi55S Y67F mutant in complex with a 5FU-RNA at 2.4 A resolution revealed formation of 5-fluoro-6-hydroxypseudouridine (5FhPsi), the same product previously seen in wild-type Psi55S-5FU-RNA complex structures. HPLC analysis confirmed efficient formation of 5FhPsi by both Psi55S Y67F and Y67L mutants but to a much lesser extent by the Y67A mutant when 5FU-RNA substrate was used. However, both HPLC analysis and a tritium release assay indicated that these mutants had no detectable enzymatic activity when the natural RNA substrate was used. The combined structural and mutational studies lead us to propose that the side chain of the conserved tyrosine in these four families of PsiS plays a dual role within the active site, maintaining the structural integrity of the active site through its hydrophobic phenyl ring and acting as a general base through its OH group for the proton abstraction required in the last step of PsiS-catalyzed formation of Psi.