PDBsum entry 5zyc

Isomerase

PDB id: 5zyc

Contents

Protein chain

384 a.a.

Ligands

ACT

EDO

Metals

_MN ×2

Waters ×341

PDB id:

5zyc

Name:

Isomerase

Title:

Crystal structure of glucose isomerase soaked with mn2+

Structure:

Xylose isomerase. Chain: a. Synonym: glucose isomerase. Engineered: yes

Source:

Streptomyces rubiginosus. Organism_taxid: 1929. Gene: xyla. Expressed in: streptomyces rubiginosus. Expression_system_taxid: 1929

Resolution:

1.75Å R-factor: 0.162 R-free: 0.184

Authors:

K.H.Nam

Key ref:

J.E.Bae et al. (2018). Structural analysis of substrate recognition by glucose isomerase in Mn²⁺ binding mode at M2 site in S. rubiginosus. Biochem Biophys Res Commun, 503, 770-775. PubMed id: 29909012 DOI: 10.1016/j.bbrc.2018.06.074

Date:

24-May-18 Release date: 28-Nov-18

Protein chain

P24300  (XYLA_STRRU) -  Xylose isomerase from Streptomyces rubiginosus

Seq: 388 a.a.

Struc: 384 a.a.

Enzyme reactions

• Enzyme class: E.C.5.3.1.5 - xylose isomerase.
• Reaction: alpha-D-xylose = alpha-D-xylulofuranose

alpha-D-xylose (Bound ligand (Het Group name = ACT) matches with 40.00% similarity) = alpha-D-xylulofuranose

• Cofactor: Mg(2+)

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

Key reference

DOI no: 10.1016/j.bbrc.2018.06.074

Biochem Biophys Res Commun 503:770-775 (2018)

PubMed id: 29909012

Structural analysis of substrate recognition by glucose isomerase in Mn²⁺ binding mode at M2 site in S. rubiginosus.

J.E.Bae, K.Y.Hwang, K.H.Nam.

ABSTRACT

Glucose isomerase (GI) catalyzes the reversible enzymatic isomerization of d-glucose and d-xylose to d-fructose and d-xylulose, respectively. This is one of the most important enzymes in the production of high-fructose corn syrup (HFCS) and biofuel. We recently determined the crystal structure of GI from S. rubiginosus (SruGI) complexed with a xylitol inhibitor in one metal binding mode. Although we assessed inhibitor binding at the M1 site, the metal binding at the M2 site and the substrate recognition mechanism for SruGI remains the unclear. Here, we report the crystal structure of the two metal binding modes of SruGI and its complex with glucose. This study provides a snapshot of metal binding at the SruGI M2 site in the presence of Mn²⁺, but not in the presence of Mg²⁺. Metal binding at the M2 site elicits a configuration change at the M1 site. Glucose molecule can only bind to the M1 site in presence of Mn²⁺ at the M2 site. Glucose and Mn²⁺ at the M2 site were bridged by water molecules using a hydrogen bonding network. The metal binding geometry of the M2 site indicates a distorted octahedral coordination with an angle of 55-110°, whereas the M1 site has a relatively stable octahedral coordination with an angle of 85-95°. We suggest a two-step sequential process for SruGI substrate recognition, in Mn²⁺ binding mode, at the M2 site. Our results provide a better understanding of the molecular role of the M2 site in GI substrate recognition.