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

Ji Eun Bae, Kwang Yeon Hwang, Ki Hyun Nam

Research output: Contribution to journalArticle

2 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)770-775
Number of pages6
JournalBiochemical and Biophysical Research Communications
Volume503
Issue number2
DOIs
Publication statusPublished - 2018 Sep 5

Fingerprint

xylose isomerase
Structural analysis
Metals
Substrates
Glucose
Crystal structure
Xylulose
Xylitol
Molecules
Biofuels
Xylose
Hydrogen Bonding
Isomerization
Fructose
Hydrogen bonds
Binding Sites

Keywords

  • Glucose isomerase
  • Metal binding site
  • Mn
  • Substrate
  • Xylose isomerase

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Structural analysis of substrate recognition by glucose isomerase in Mn2+ binding mode at M2 site in S. rubiginosus. / Bae, Ji Eun; Hwang, Kwang Yeon; Nam, Ki Hyun.

In: Biochemical and Biophysical Research Communications, Vol. 503, No. 2, 05.09.2018, p. 770-775.

Research output: Contribution to journalArticle

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AB - 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.

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