8FDB | pdb_00008fdb

CRYSTAL STRUCTURE OF NAGB-II PHOSPHOSUGAR ISOMERASE FROM Shewanella denitrificans OS217 IN COMPLEX WITH GLUCITOLAMINE-6-PHOSPHATE AT 3.06 A RESOLUTION.

PDB DOI: https://doi.org/10.2210/pdb8FDB/pdb

Classification: ISOMERASE
Organism(s): Shewanella denitrificans OS217
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-02 Released: 2023-05-17
Deposition Author(s): Rodriguez-Romero, A., Rodriguez-Hernandez, A., Marcos-Viquez, J., Bustos-Jaimes, I.
Funding Organization(s): Consejo Nacional de Ciencia y Tecnologia (CONACYT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.06 Å
R-Value Free:
0.241 (Depositor), 0.242 (DCC)
R-Value Work:
0.206 (Depositor), 0.206 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Substrate binding in the allosteric site mimics homotropic cooperativity in the SIS-fold glucosamine-6-phosphate deaminases.

Marcos-Viquez, J., Rodriguez-Hernandez, A., Alvarez-Anorve, L.I., Medina-Garcia, A., Plumbridge, J., Calcagno, M.L., Rodriguez-Romero, A., Bustos-Jaimes, I.

(2023) Protein Sci 32: e4651-e4651

PubMed: 37145875 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.4651
Primary Citation Related Structures:
8EOL, 8EYM, 8FDB

PubMed Abstract:
Glucosamine-6-phosphate (GlcN6P) deaminases from Escherichia coli (EcNagBI) and Shewanella denitrificans (SdNagBII) are special examples of what constitute nonhomologous isofunctional enzymes due to their convergence, not only in catalysis, but also in cooperativity and allosteric properties. Additionally, we found that the sigmoidal kinetics of SdNagBII cannot be explained by the existing models of homotropic activation. This study describes the regulatory mechanism of SdNagBII using enzyme kinetics, isothermal titration calorimetry (ITC), and X-ray crystallography. ITC experiments revealed two different binding sites with distinctive thermodynamic signatures: a single binding site per monomer for the allosteric activator N-acetylglucosamine 6-phosphate (GlcNAc6P) and two binding sites per monomer for the transition-state analog 2-amino-2-deoxy-D-glucitol 6-phosphate (GlcNol6P). Crystallographic data demonstrated the existence of an unusual allosteric site that can bind both GlcNAc6P and GlcNol6P, implying that the homotropic activation of this enzyme arises from the occupation of the allosteric site by the substrate. In this work we describe the presence of this novel allosteric site in the SIS-fold deaminases, which is responsible for the homotropic and heterotropic activation of SdNagBII by GlcN6P and GlcNAc6P, respectively. This study unveils an original mechanism to generate a high degree of homotropic activation in SdNagBII, mimicking the allosteric and cooperative properties of hexameric EcNagBI but with a reduced number of subunits.

Organizational Affiliation

Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.

Macromolecule Content

Total Structure Weight: 72.27 kDa
Atom Count: 5,010
Modeled Residue Count: 665
Deposited Residue Count: 666
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine-fructose-6-phosphate transaminase (Isomerizing)	A	333	Shewanella denitrificans OS217	Mutation(s): 0 Gene Names: Sden_2705 EC: 2.6.1.16
UniProt
Find proteins for Q12KP2 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)) Explore Q12KP2 Go to UniProtKB: Q12KP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12KP2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine-fructose-6-phosphate transaminase (Isomerizing)	B	333	Shewanella denitrificans OS217	Mutation(s): 0 Gene Names: Sden_2705 EC: 2.6.1.16
UniProt
Find proteins for Q12KP2 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)) Explore Q12KP2 Go to UniProtKB: Q12KP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12KP2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGP (Subject of Investigation/LOI) Query on AGP Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], H [auth B], I [auth B]	2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE C₆ H₁₆ N O₈ P LBNVXZROMBUNNQ-SLPGGIOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth B]	G [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain J [auth B] Interactions & Density Focus chain G [auth B] Focus chain J [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]