4Z0H

X-ray structure of cytoplasmic glyceraldehyde-3-phosphate dehydrogenase (GapC1) complexed with NAD

PDB DOI: https://doi.org/10.2210/pdb4Z0H/pdb

Classification: OXIDOREDUCTASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-03-26 Released: 2016-04-13
Deposition Author(s): Fermani, S., Zaffagnini, M., Orru, R., Falini, G., Trost, P.
Funding Organization(s): University of Bologna

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.278
R-Value Work: 0.249
R-Value Observed: 0.251

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Tuning Cysteine Reactivity and Sulfenic Acid Stability by Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis thaliana.

Zaffagnini, M., Fermani, S., Calvaresi, M., Orru, R., Iommarini, L., Sparla, F., Falini, G., Bottoni, A., Trost, P.

(2016) Antioxid Redox Signal 24: 502-517

PubMed: 26650776 Search on PubMed
DOI: https://doi.org/10.1089/ars.2015.6417
Primary Citation of Related Structures:
4Z0H

PubMed Abstract:
Cysteines and H2O2 are fundamental players in redox signaling. Cysteine thiol deprotonation favors the reaction with H2O2 that generates sulfenic acids with dual electrophilic/nucleophilic nature. The protein microenvironment surrounding the target cysteine is believed to control whether sulfenic acid can be reversibly regulated by disulfide formation or irreversibly oxidized to sulfinates/sulfonates. In this study, we present experimental oxidation kinetics and a quantum mechanical/molecular mechanical (QM/MM) investigation to elucidate the reaction of H2O2 with glycolytic and photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis thaliana (cytoplasmic AtGAPC1 and chloroplastic AtGAPA, respectively).

Organizational Affiliation

1 Department of Pharmacy and Biotechnology, University of Bologna , Bologna, Italy.

Macromolecule Content

Total Structure Weight: 75.03 kDa
Atom Count: 5,433
Modelled Residue Count: 667
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic	A [auth O], B [auth R]	334	Arabidopsis thaliana	Mutation(s): 0 Gene Names: GAPC1, GAPC, GAPDH, At3g04120, T6K12.26 EC: 1.2.1.12
UniProt
Find proteins for P25858 (Arabidopsis thaliana) Explore P25858 Go to UniProtKB: P25858
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25858
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain C [auth O] SDF format, chain G [auth R] MOL2 format, chain C [auth O] MOL2 format, chain G [auth R]	C [auth O], G [auth R]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth O] Focus chain G [auth R] Interactions & Density Focus chain C [auth O] Focus chain G [auth R]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth O] SDF format, chain E [auth O] SDF format, chain F [auth O] SDF format, chain H [auth R] SDF format, chain I [auth R] SDF format, chain J [auth R] SDF format, chain K [auth R] MOL2 format, chain D [auth O] MOL2 format, chain E [auth O] MOL2 format, chain F [auth O] MOL2 format, chain H [auth R] MOL2 format, chain I [auth R] MOL2 format, chain J [auth R] MOL2 format, chain K [auth R]	D [auth O] E [auth O] F [auth O] H [auth R] I [auth R] D [auth O], E [auth O], F [auth O], H [auth R], I [auth R], J [auth R], K [auth R]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth O] Focus chain E [auth O] Focus chain F [auth O] Focus chain H [auth R] Focus chain I [auth R] Focus chain J [auth R] Focus chain K [auth R] Interactions & Density Focus chain D [auth O] Focus chain E [auth O] Focus chain F [auth O] Focus chain H [auth R] Focus chain I [auth R] Focus chain J [auth R] Focus chain K [auth R]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.278
R-Value Work: 0.249
R-Value Observed: 0.251
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.849	α = 90
b = 76.849	β = 90
c = 406.626	γ = 120

Software Package:

Software Name	Purpose
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Funding Organization	Location	Grant Number
University of Bologna	Italy	FARB2012Francia

Revision History (Full details and data files)

Version 1.0: 2016-04-13
Type: Initial release
Version 1.1: 2017-04-12
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description