PDBsum entry 6ynh

Biosynthetic protein

PDB id: 6ynh

Contents

Protein chains

334 a.a.

Ligands

XPE ×4

Waters ×132

PDB id:

6ynh

Name:

Biosynthetic protein

Title:

Gapdh purified from the supernatant of hek293f cells: crystal form 4 of 4

Structure:

Glyceraldehyde-3-phosphate dehydrogenase. Chain: b, d, f, g. Synonym: gapdh,peptidyl-cysteine s-nitrosylase gapdh. Ec: 1.2.1.12,2.6.99.-

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cell_line: hek293f. Organ: kidney. Tissue: epithelium

Resolution:

2.62Å R-factor: 0.178 R-free: 0.215

Authors:

P.Roversi,A.Lia

Key ref:

A.Lia et al. (2020). Partial catalytic Cys oxidation of human GAPDH to Cys-sulfonic acid. Wellcome Open Res, 5, 114. PubMed id: 32802964 DOI: 10.12688/wellcomeopenres.15893.2

Date:

13-Apr-20 Release date: 06-May-20

Protein chains

P04406  (G3P_HUMAN) -  Glyceraldehyde-3-phosphate dehydrogenase from Homo sapiens

Seq: 335 a.a.

Struc: 334 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 1: E.C.1.2.1.12 - glyceraldehyde-3-phosphate dehydrogenase (phosphorylating).
• Pathway: Glyceraldehyde-3-phosphate Dehydrogenase (phosphorylating)
• Reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD⁺ = (2R)-3-phospho- glyceroyl phosphate + NADH + H⁺
• Enzyme class 2: E.C.2.6.99.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.12688/wellcomeopenres.15893.2

Wellcome Open Res 5:114 (2020)

PubMed id: 32802964

Partial catalytic Cys oxidation of human GAPDH to Cys-sulfonic acid.

A.Lia, A.Dowle, C.Taylor, A.Santino, P.Roversi.

ABSTRACT

Background: n-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyses the NAD ⁺-dependent oxidative phosphorylation of n-glyceraldehyde-3-phosphate to 1,3-diphospho-n-glycerate and its reverse reaction in glycolysis and gluconeogenesis. Methods: Four distinct crystal structures of human n-Glyceraldehyde-3-phosphate dehydrogenase ( HsGAPDH) have been determined from protein purified from the supernatant of HEK293F human epithelial kidney cells. Results: X-ray crystallography and mass-spectrometry indicate that the catalytic cysteine of the protein ( HsGAPDH Cys152) is partially oxidised to cysteine S-sulfonic acid. The average occupancy for the Cys152-S-sulfonic acid modification over the 20 crystallographically independent copies of HsGAPDH across three of the crystal forms obtained is 0.31±0.17. Conclusions: The modification induces no significant structural changes on the tetrameric enzyme, and only makes aspecific contacts to surface residues in the active site, in keeping with the hypothesis that the oxidising conditions of the secreted mammalian cell expression system result in HsGAPDH catalytic cysteine S-sulfonic acid modification and irreversible inactivation of the enzyme.