5ZA0

A cryo-protectant induces the conformational change of glyceraldehyde-3-phosphate dehydrogenase

  • Classification: OXIDOREDUCTASE
  • Organism(s): Escherichia coli K-12
  • Mutation(s): No 

  • Deposited: 2018-02-06 Released: 2018-05-30 
  • Deposition Author(s): Kim, Y.J.
  • Funding Organization(s): National Research Foundation of Korea, Chonbuk National University

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

A cryoprotectant induces conformational change in glyceraldehyde-3-phosphate dehydrogenase.

Kim, Y.J.

(2018) Acta Crystallogr F Struct Biol Commun 74: 277-282

  • DOI: https://doi.org/10.1107/S2053230X18004557
  • Primary Citation of Related Structures:  
    5ZA0

  • PubMed Abstract: 

    Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme, catalyses the conversion of D-glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate. While mammalian and yeast GAPDHs are multifunctional proteins that have additional functions beyond those involved in glycolysis, including reactions related to nuclear RNA transport, DNA replication/repair, membrane fusion and cellular apoptosis, Escherichia coli GAPDH (ecGAPDH) has only been reported to function in glycolysis. The S-loop of GAPDH is required for interaction with its cofactor and with other proteins. In this study, the three-dimensional crystal structure of GAPDH treated with trehalose is reported at 2.0 Å resolution. Trehalose was used as a cryoprotectant for the GAPDH crystals. The structure of trehalose-bound ecGAPDH was compared with the structures of both NAD + -free and NAD + -bound ecGAPDH. At the S-loop, the bound trehalose in the GAPDH structure induces a 2.4° rotation compared with the NAD + -free ecGAPDH structure and a 3.1° rotation compared with the NAD + -bound ecGAPDH structure.


  • Organizational Affiliation

    Department of Herbal Medicine Resources, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase A331Escherichia coli K-12Mutation(s): 0 
EC: 1.2.1.12
UniProt
Find proteins for P0A9B2 (Escherichia coli (strain K12))
Explore P0A9B2 
Go to UniProtKB:  P0A9B2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9B2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G92130SN
GlyCosmos:  G92130SN
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.295α = 90
b = 121.295β = 90
c = 156.056γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2018-05-30 
  • Deposition Author(s): Kim, Y.J.

Funding OrganizationLocationGrant Number
National Research Foundation of KoreaKorea, Republic Of2015R1C1A1A02037509
Chonbuk National UniversityKorea, Republic OfJeon-Dae Memorial Fund in 2014

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary