PDBsum entry 1a7k

Oxidoreductase

PDB id: 1a7k

Contents

Protein chains

358 a.a. *

Ligands

PO4 ×8

NAD ×4

* Residue conservation analysis

PDB id:

1a7k

Name:

Oxidoreductase

Title:

Glycosomal glyceraldehyde-3-phosphate dehydrogenase in a monoclinic crystal form

Structure:

Glyceraldehyde-3-phosphate dehydrogenase. Chain: a, b, c, d. Synonym: gapdh. Engineered: yes. Other_details: one bound NAD and two bound phosphates per monomer

Source:

Leishmania mexicana. Organism_taxid: 5665. Cell_line: bl21. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.80Å R-factor: 0.217 R-free: 0.292

Authors:

H.Kim,W.G.J.Hol

Key ref:

H.Kim and W.G.Hol (1998). Crystal structure of Leishmania mexicana glycosomal glyceraldehyde-3-phosphate dehydrogenase in a new crystal form confirms the putative physiological active site structure. J Mol Biol, 278, 5. PubMed id: 9571030 DOI: 10.1006/jmbi.1998.1661

Date:

16-Mar-98 Release date: 17-Jun-98

Protein chains

Q27890  (G3PG_LEIME) -  Glyceraldehyde-3-phosphate dehydrogenase, glycosomal from Leishmania mexicana

Seq: 361 a.a.

Struc: 358 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⁺

D-glyceraldehyde 3-phosphate + phosphate (Bound ligand (Het Group name = NAD) corresponds exactly) + NAD(+) (Bound ligand (Het Group name = PO4) corresponds exactly) = (2R)-3-phospho- glyceroyl phosphate + NADH + H(+)

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

reference

DOI no: 10.1006/jmbi.1998.1661

J Mol Biol 278:5 (1998)

PubMed id: 9571030

Crystal structure of Leishmania mexicana glycosomal glyceraldehyde-3-phosphate dehydrogenase in a new crystal form confirms the putative physiological active site structure.

H.Kim, W.G.Hol.

ABSTRACT

The structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the trypanosomatid parasite Leishmania mexicana in a new crystal form has been determined by X-ray crystallography. The protein crystallizes in space group P21 with one 156 kDa tetramer per asymmetric unit. The model of the protein with bound NAD+s and phosphates has been refined against 81% complete data from 10.0 to 2. 8 A to a crystallographic Rfactor of 0.217. The present structure confirms two key aspects of the previously reported orthorhombic crystal structure of L. mexicana GAPDH (LmGAPDH): the unusual conformation of a loop in the active site, and the repositioning of the inorganic phosphate binding site compared with crystal structures of GAPDHs from other organisms. As the monoclinic crystals of LmGAPDH were grown at a phosphate concentration and pH that were even closer to physiological conditions than were the orthorhombic LmGAPDH crystals, the present structure reinforces the physiological relevance of the active site structure seen in the previous orthorhombic crystal of LmGAPDH.

Selected figure(s)

Figure 2.
Figure 2. Stereoview of 220s loop in monoclinic LmGAPDH. (a) Simulated annealing omit Fo - Fc electron density map (Hodel et al., 1992; Read, 1986) of monoclinic LmGAPDH for which Pro223 to Ala228 were omitted from the Fc calculations. The map contour level is 2.0s. Superimposed on the electron density is the refined conformation of the 220s loop in monoclinic LmGAPDH. (b) Superposition of monoclinic and orthorhombic LmGAPDHs at the 220s loop region. Monoclinic LmGAPDH is drawn in thick lightly shaded bonds. Orthorhom- bic LmGAPDH is drawn in thin filled bonds. This figure was made with MOLSCRIPT.

Figure 3.
Figure 3. Representative Rama- chandran plot of the A subunit of LmGAPDH in the monoclinic crys- tal form. Glycine residues are indi- cated with hollow circles, all other residues with filled circles. The resi- dues in the 220s loop, Pro223 to Ala228 are labelled.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 278, 5-0) copyright 1998.

Figures were selected by an automated process.