3W0L | pdb_00003w0l

The crystal structure of Xenopus Glucokinase and Glucokinase Regulatory Protein complex

PDB DOI: https://doi.org/10.2210/pdb3W0L/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Xenopus laevis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-10-31 Released: 2013-07-17
Deposition Author(s): Choi, J.M., Seo, M.H., Kyeong, H.H., Kim, E., Kim, H.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.92 Å
R-Value Free:
0.277 (Depositor), 0.272 (DCC)
R-Value Work:
0.242 (Depositor), 0.233 (DCC)
R-Value Observed:
0.244 (Depositor)

Starting Models: experimental
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Ligand Structure Quality Assessment

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

Literature

Molecular basis for the role of glucokinase regulatory protein as the allosteric switch for glucokinase

Choi, J.M., Seo, M.H., Kyeong, H.H., Kim, E., Kim, H.S.

(2013) Proc Natl Acad Sci U S A 110: 10171-10176

PubMed: 23733961 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.1300457110
Primary Citation Related Structures:
3W0L

PubMed Abstract:
Glucokinase (GK) is a monomeric allosteric enzyme and plays a pivotal role in blood glucose homeostasis. GK is regulated by GK regulatory protein (GKRP), and indirectly by allosteric effectors of GKRP. Despite the critical roles of GK and GKRP, the molecular basis for the allosteric regulation mechanism of GK by GKRP remains unclear. We determined the crystal structure of Xenopus GK and GKRP complex in the presence of fructose-6-phosphate at 2.9 Å. GKRP binds to a super-open conformation of GK mainly through hydrophobic interaction, inhibiting the GK activity by locking a small domain of GK. We demonstrate the molecular mechanism for the modulation of GK activity by allosteric effectors of GKRP. Importantly, GKRP releases GK in a sigmoidal manner in response to glucose concentration by restricting a structural rearrangement of the GK small domain via a single ion pair. We find that GKRP acts as an allosteric switch for GK in blood glucose control by the liver.

Organizational Affiliation

Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea.

Macromolecule Content

Total Structure Weight: 240.87 kDa
Atom Count: 15,800
Modeled Residue Count: 2,008
Deposited Residue Count: 2,154
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A, C	458	Xenopus laevis	Mutation(s): 0 Gene Names: gck EC: 2.7.1.2 (PDB Primary Data), 2.7.1 (UniProt)
UniProt
Find proteins for Q91753 (Xenopus laevis) Explore Q91753 Go to UniProtKB: Q91753
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q91753
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase regulatory protein	B, D	619	Xenopus laevis	Mutation(s): 0 Gene Names: gckr
UniProt
Find proteins for Q91754 (Xenopus laevis) Explore Q91754 Go to UniProtKB: Q91754
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q91754
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F6R Query on F6R Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain L [auth D] MOL2 format, chain G [auth B] MOL2 format, chain L [auth D] mmCIF format, chain G [auth B] mmCIF format, chain L [auth D]	G [auth B], L [auth D]	FRUCTOSE -6-PHOSPHATE C₆ H₁₃ O₉ P GSXOAOHZAIYLCY-HSUXUTPPSA-N		Interactions Focus chain G [auth B] Focus chain L [auth D] Interactions & Density Focus chain G [auth B] Focus chain L [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C]	E [auth A], H [auth B], I [auth B], J [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth C]	F [auth A], K [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.92 Å
R-Value Free: 0.277 (Depositor), 0.272 (DCC)
R-Value Work: 0.242 (Depositor), 0.233 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.318	α = 90
b = 130.03	β = 90
c = 175.117	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-07-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-17
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description