PDBsum entry 1vsu

Oxidoreductase

PDB id: 1vsu

Contents

Protein chains

325 a.a. *

Waters ×405

* Residue conservation analysis

PDB id:

1vsu

Name:

Oxidoreductase

Title:

Crystal structure of apo-glyceraldehyde 3-phosphate dehydrogenase from cryptosporidium parvum

Structure:

Glyceraldehyde-3-phosphate dehydrogenase. Chain: a, b, c, d. Synonym: gapdh. Engineered: yes

Source:

Cryptosporidium parvum. Organism_taxid: 5807. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å R-factor: 0.203 R-free: 0.245

Authors:

W.J.Cook,O.Senkovich,D.Chattopadhyay

Key ref:

W.J.Cook et al. (2009). An unexpected phosphate binding site in glyceraldehyde 3-phosphate dehydrogenase: crystal structures of apo, holo and ternary complex of Cryptosporidium parvum enzyme. Bmc Struct Biol, 9, 9-9. PubMed id: 19243605

Date:

10-Mar-08 Release date: 24-Mar-09

Supersedes:

3chz

Protein chains

Q7YYQ9  (Q7YYQ9_CRYPV) -  Glyceraldehyde-3-phosphate dehydrogenase from Cryptosporidium parvum

Seq: 339 a.a.

Struc: 325 a.a.

Enzyme reactions

• Enzyme class: 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⁺

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

reference

Bmc Struct Biol 9:9-9 (2009)

PubMed id: 19243605

An unexpected phosphate binding site in glyceraldehyde 3-phosphate dehydrogenase: crystal structures of apo, holo and ternary complex of Cryptosporidium parvum enzyme.

W.J.Cook, O.Senkovich, D.Chattopadhyay.

ABSTRACT

BACKGROUND: The structure, function and reaction mechanism of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) have been extensively studied. Based on these studies, three anion binding sites have been identified, one 'Ps' site (for binding the C-3 phosphate of the substrate) and two sites, 'Pi' and 'new Pi', for inorganic phosphate. According to the original flip-flop model, the substrate phosphate group switches from the 'Pi' to the 'Ps' site during the multistep reaction. In light of the discovery of the 'new Pi' site, a modified flip-flop mechanism, in which the C-3 phosphate of the substrate binds to the 'new Pi' site and flips to the 'Ps' site before the hydride transfer, was proposed. An alternative model based on a number of structures of B. stearothermophilus GAPDH ternary complexes (non-covalent and thioacyl intermediate) proposes that in the ternary Michaelis complex the C-3 phosphate binds to the 'Ps' site and flips from the 'Ps' to the 'new Pi' site during or after the redox step. RESULTS: We determined the crystal structure of Cryptosporidium parvum GAPDH in the apo and holo (enzyme + NAD) state and the structure of the ternary enzyme-cofactor-substrate complex using an active site mutant enzyme. The C. parvum GAPDH complex was prepared by pre-incubating the enzyme with substrate and cofactor, thereby allowing free movement of the protein structure and substrate molecules during their initial encounter. Sulfate and phosphate ions were excluded from purification and crystallization steps. The quality of the electron density map at 2A resolution allowed unambiguous positioning of the substrate. In three subunits of the homotetramer the C-3 phosphate group of the non-covalently bound substrate is in the 'new Pi' site. A concomitant movement of the phosphate binding loop is observed in these three subunits. In the fourth subunit the C-3 phosphate occupies an unexpected site not seen before and the phosphate binding loop remains in the substrate-free conformation. Orientation of the substrate with respect to the active site histidine and serine (in the mutant enzyme) also varies in different subunits. CONCLUSION: The structures of the C. parvum GAPDH ternary complex and other GAPDH complexes demonstrate the plasticity of the substrate binding site. We propose that the active site of GAPDH can accommodate the substrate in multiple conformations at multiple locations during the initial encounter. However, the C-3 phosphate group clearly prefers the 'new Pi' site for initial binding in the active site.