5ZYD | pdb_00005zyd

Crystal Structure of Glucose Isomerase Soaked with Glucose

PDB DOI: https://doi.org/10.2210/pdb5ZYD/pdb

Classification: ISOMERASE
Organism(s): Streptomyces pseudogriseolus
Expression System: Streptomyces pseudogriseolus
Mutation(s): No

Deposited: 2018-05-24 Released: 2018-11-28
Deposition Author(s): Nam, K.H.
Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.165 (Depositor), 0.172 (DCC)
R-Value Work:
0.151 (Depositor), 0.159 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

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

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

PubMed: 29909012 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2018.06.074
Primary Citation Related Structures:
5ZYC, 5ZYD, 5ZYE

PubMed 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 Mn ²⁺, but not in the presence of Mg ²⁺. 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 Mn ²⁺ at the M2 site. Glucose and Mn ²⁺ 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 Mn ²⁺ binding mode, at the M2 site. Our results provide a better understanding of the molecular role of the M2 site in GI substrate recognition.

Organizational Affiliation

School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, Republic of Korea.

Macromolecule Content

Total Structure Weight: 43.37 kDa
Atom Count: 3,684
Modeled Residue Count: 384
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A	388	Streptomyces pseudogriseolus	Mutation(s): 0 Gene Names: xylA EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces pseudogriseolus) Explore P24300 Go to UniProtKB: P24300
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24300
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.165 (Depositor), 0.172 (DCC)
R-Value Work: 0.151 (Depositor), 0.159 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.505	α = 90
b = 97.82	β = 90
c = 102.297	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-11-28

Deposition Author(s):

Nam, K.H.

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017R1D1A1B03033087
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017M3A9F6029736