PDBsum entry 4xsl

Isomerase

PDB id: 4xsl

Contents

Protein chains

294 a.a.

Ligands

GOL ×14

Metals

_MN ×4

Waters ×1268

PDB id:

4xsl

Name:

Isomerase

Title:

Crystal strcutre of d-tagatose 3-epimerase c66s from pseudomonas cichorii in complex with glycerol

Structure:

D-tagatose 3-epimerase. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Pseudomonas cichorii. Organism_taxid: 36746. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.60Å R-factor: 0.178 R-free: 0.205

Authors:

H.Yoshida,A.Yoshihara,T.Ishii,K.Izumori,S.Kamitori

Key ref:

H.Yoshida et al. (2016). X-ray structures of the Pseudomonas cichorii D-tagatose 3-epimerase mutant form C66S recognizing deoxy sugars as substrates. Appl Microbiol Biotechnol, 100, 10403-10415. PubMed id: 27368739 DOI: 10.1007/s00253-016-7673-7

Date:

22-Jan-15 Release date: 27-Jan-16

Protein chains

O50580  (DT3E_PSECI) -  D-tagatose 3-epimerase from Pseudomonas cichorii

Seq: 290 a.a.

Struc: 294 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.5.1.3.31 - D-tagatose 3-epimerase.
• Reaction:
  1. keto-D-tagatose = keto-D-sorbose
  2. D-allulose = keto-D-fructose

D-allulose (Bound ligand (Het Group name = GOL) matches with 50.00% similarity) = keto-D-fructose

• Cofactor: Mn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1007/s00253-016-7673-7

Appl Microbiol Biotechnol 100:10403-10415 (2016)

PubMed id: 27368739

X-ray structures of the Pseudomonas cichorii D-tagatose 3-epimerase mutant form C66S recognizing deoxy sugars as substrates.

H.Yoshida, A.Yoshihara, T.Ishii, K.Izumori, S.Kamitori.

ABSTRACT

Pseudomonas cichorii D-tagatose 3-epimerase (PcDTE), which has a broad substrate specificity, efficiently catalyzes the epimerization of not only D-tagatose to D-sorbose but also D-fructose to D-psicose (D-allulose) and also recognizes the deoxy sugars as substrates. In an attempt to elucidate the substrate recognition and catalytic reaction mechanisms of PcDTE for deoxy sugars, the X-ray structures of the PcDTE mutant form with the replacement of Cys66 by Ser (PcDTE_C66S) in complexes with deoxy sugars were determined. These X-ray structures showed that substrate recognition by the enzyme at the 1-, 2-, and 3-positions is responsible for enzymatic activity and that substrate-enzyme interactions at the 4-, 5-, and 6-positions are not essential for the catalytic reaction of the enzyme leading to the broad substrate specificity of PcDTE. They also showed that the epimerization site of 1-deoxy 3-keto D-galactitol is shifted from C3 to C4 and that 1-deoxy sugars may bind to the catalytic site in the inhibitor-binding mode. The hydrophobic groove that acts as an accessible surface for substrate binding is formed through the dimerization of PcDTE. In PcDTE_C66S/deoxy sugar complex structures, bound ligand molecules in both the linear and ring forms were detected in the hydrophobic groove, while bound ligand molecules in the catalytic site were in the linear form. This result suggests that the sugar-ring opening of a substrate may occur in the hydrophobic groove and also that the narrow channel of the passageway to the catalytic site allows a substrate in the linear form to pass through.