PDBsum entry: 1ky8

Oxidoreductase

PDB id: 1ky8

Contents

Protein chain

499 a.a. *

Ligands

NAP

Metals

_NA

Waters ×386

* Residue conservation analysis

PDB id:

1ky8

Name:

Oxidoreductase

Title:

Crystal structure of the non-phosphorylating glyceraldehyde- phosphate dehydrogenase

Structure:

Glyceraldehyde-3-phosphate dehydrogenase. Chain: a. Synonym: NADP+. Engineered: yes

Source:

Thermoproteus tenax. Organism_taxid: 2271. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.40Å R-factor: 0.208 R-free: 0.242

Authors:

E.Pohl,N.Brunner,M.Wilmanns,R.Hensel

Key ref:

E.Pohl et al. (2002). The crystal structure of the allosteric non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeum Thermoproteus tenax. J Biol Chem, 277, 19938-19945. PubMed id: 11842090 DOI: 10.1074/jbc.M112244200

Date:

04-Feb-02 Release date: 04-Feb-03

Protein chain

O57693  (O57693_THETE) -  Glyceraldehyde-3-phosphate dehydrogenase (NADP+)

Seq: 501 a.a.

Struc: 499 a.a.

Enzyme reactions

• Enzyme class: E.C.1.2.1.9 - Glyceraldehyde-3-phosphate dehydrogenase (NADP(+)).
• Reaction: D-glyceraldehyde 3-phosphate + NADP⁺ + H₂O = 3-phospho-D-glycerate + NADPH

D-glyceraldehyde 3-phosphate + NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) + H(2)O = 3-phospho-D-glycerate + NADPH

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

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (2 terms)
• Biochemical function: nucleotide binding (4 terms)

reference

DOI no: 10.1074/jbc.M112244200

J Biol Chem 277:19938-19945 (2002)

PubMed id: 11842090

The crystal structure of the allosteric non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeum Thermoproteus tenax.

E.Pohl, N.Brunner, M.Wilmanns, R.Hensel.

ABSTRACT

The NAD(+)-dependent non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) from the hyperthermophilic archaeum Thermoproteus tenax represents an archaeal member of the diverse superfamily of aldehyde dehydrogenases (ALDHs). GAPN catalyzes the irreversible oxidation of d-glyceraldehyde 3-phosphate to 3-phosphoglycerate. In this study, we present the crystal structure of GAPN in complex with its natural inhibitor NADP(+) determined by multiple anomalous diffraction methods. The structure was refined to a resolution of 2.4 A with an R-factor of 0.21. The overall fold of GAPN is similar to the structures of ALDHs described previously, consisting of three domains: a nucleotide-binding domain, a catalytic domain, and an oligomerization domain. Local differences in the active site are responsible for substrate specificity. The inhibitor NADP(+) binds at an equivalent site to the cosubstrate-binding site of other ALDHs and blocks the enzyme in its inactive state, possibly preventing the transition to the active conformation. Structural comparison between GAPN from the hyperthermophilic T. tenax and homologs of mesophilic organisms establishes several characteristics of thermostabilization. These include protection against heat-induced covalent modifications by reducing and stabilizing labile residues, a decrease in number and volume of empty cavities, an increase in beta-strand content, and a strengthening of subunit contacts by ionic and hydrophobic interactions.

Selected figure(s)

Figure 3.
Fig. 3. Least-squares superposition of structurally equivalent C^ atoms of Tt-GAPN (red) and Sm-GAPN (blue) (10).

Figure 4.
Fig. 4. a, stereo view of a representative portion of the experimental electron density map after solvent flattening at a 1.5- level showing the inhibitor-binding site. The final model of NADP+ is superimposed as a ball-and-stick representation. b, close-up stereo view of the binding site showing the hydrogen bonds between the phosphate and protein atoms. The nicotinamide moiety has been omitted for clarity. c, position of NADP+ in the structures of Tt-GAPN ( gray bonds) and Sm-GAPN (white bonds) after the least-squares superposition of the C^ trace of the two enzymes.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 19938-19945) copyright 2002.

Figures were selected by an automated process.