PDBsum entry 6j7c

Isomerase

PDB id: 6j7c

Contents

Protein chain

331 a.a.

Ligands

PRO

Waters ×29

PDB id:

6j7c

Name:

Isomerase

Title:

Crystal structure of proline racemase-like protein from thermococcus litoralis in complex with proline

Structure:

Proline racemase. Chain: a. Engineered: yes

Source:

Thermococcus litoralis (strain atcc 51850 / dsm 5473 / jcm 8560 / ns-c). Organism_taxid: 523849. Strain: atcc 51850 / dsm 5473 / jcm 8560 / ns-c. Gene: occ_00372. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.70Å R-factor: 0.251 R-free: 0.296

Authors:

Y.Watanabe,S.Watanabe,Y.Itoh,Y.Watanabe

Key ref:

Y.Watanabe et al. (2019). Crystal structure of substrate-bound bifunctional proline racemase/hydroxyproline epimerase from a hyperthermophilic archaeon. Biochem Biophys Res Commun, 511, 135-140. PubMed id: 30773259 DOI: 10.1016/j.bbrc.2019.01.141

Date:

17-Jan-19 Release date: 27-Feb-19

Protein chain

H3ZMH5  (H3ZMH5_THELN) -  Proline racemase from Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C)

Seq: 331 a.a.

Struc: 331 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1016/j.bbrc.2019.01.141

Biochem Biophys Res Commun 511:135-140 (2019)

PubMed id: 30773259

Crystal structure of substrate-bound bifunctional proline racemase/hydroxyproline epimerase from a hyperthermophilic archaeon.

Y.Watanabe, S.Watanabe, Y.Itoh, Y.Watanabe.

ABSTRACT

The hypothetical OCC_00372 protein from Thermococcus litoralis is a member of the ProR superfamily from hyperthermophilic archaea and exhibits unique bifunctional proline racemase/hydroxyproline 2-epimerase activity. However, the molecular mechanism of the broad substrate specificity and extreme thermostability of this enzyme (TlProR) remains unclear. Here we determined the crystal structure of TlProR at 2.7 Å resolution. Of note, a substrate proline molecule, derived from expression host Escherichia coli cells, was tightly bound in the active site of TlProR. The substrate bound structure and mutational analyses suggested that Trp241 is involved in hydroxyproline recognition by making a hydrogen bond between the indole group of Trp241 and the hydroxyl group of hydroxyproline. Additionally, Tyr171 may contribute to the thermostability by making hydrogen bonds between the hydroxyl group of Tyr171 and catalytic residues. Our structural and functional analyses provide a structural basis for understanding the molecular mechanism of substrate specificity and thermostability of ProR superfamily proteins.