PDBsum entry 1a80

Oxidoreductase

PDB id: 1a80

Contents

Protein chain

277 a.a. *

Ligands

NDP

Waters ×105

* Residue conservation analysis

PDB id:

1a80

Name:

Oxidoreductase

Title:

Native 2,5-diketo-d-gluconic acid reductase a from corynbacterium sp. Complexed with NADPH

Structure:

2,5-diketo-d-gluconic acid reductase a. Chain: a. Synonym: 2,5-dkg reductase a. Engineered: yes

Source:

Corynebacterium sp.. Organism_taxid: 1720. Variant: a. Gene: 2 5-diketo-d-gluconic acid. Expressed in: pantoea citrea. Expression_system_taxid: 53336.

Resolution:

2.10Å R-factor: 0.191 R-free: 0.288

Authors:

S.Khurana,D.B.Powers,S.Anderson,M.Blaber

Key ref:

S.Khurana et al. (1998). Crystal structure of 2,5-diketo-D-gluconic acid reductase A complexed with NADPH at 2.1-A resolution. Proc Natl Acad Sci U S A, 95, 6768-6773. PubMed id: 9618487 DOI: 10.1073/pnas.95.12.6768

Date:

31-Mar-98 Release date: 30-Mar-99

Protein chain

P06632  (DKGA_CORSC) -  2,5-diketo-D-gluconic acid reductase A from Corynebacterium sp. (strain ATCC 31090)

Seq: 278 a.a.

Struc: 277 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.346 - 2,5-didehydrogluconate reductase (2-dehydro-L-gulonate-forming).
• Reaction: 2-dehydro-L-idonate + NADP⁺ = 2,5-didehydro-D-gluconate + NADPH + H⁺

2-dehydro-L-idonate + NADP(+) (Bound ligand (Het Group name = NDP) corresponds exactly) = 2,5-didehydro-D-gluconate + NADPH + H(+)

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

reference

DOI no: 10.1073/pnas.95.12.6768

Proc Natl Acad Sci U S A 95:6768-6773 (1998)

PubMed id: 9618487

Crystal structure of 2,5-diketo-D-gluconic acid reductase A complexed with NADPH at 2.1-A resolution.

S.Khurana, D.B.Powers, S.Anderson, M.Blaber.

ABSTRACT

The three-dimensional structure of Corynebacterium 2, 5-diketo-D-gluconic acid reductase A (2,5-DKGR A; EC 1.1.1.-), in complex with cofactor NADPH, has been solved by using x-ray crystallographic data to 2.1-A resolution. This enzyme catalyzes stereospecific reduction of 2,5-diketo-D-gluconate (2,5-DKG) to 2-keto-L-gulonate. Thus the three-dimensional structure has now been solved for a prokaryotic example of the aldo-keto reductase superfamily. The details of the binding of the NADPH cofactor help to explain why 2,5-DKGR exhibits lower binding affinity for cofactor than the related human aldose reductase does. Furthermore, changes in the local loop structure near the cofactor suggest that 2,5-DKGR will not exhibit the biphasic cofactor binding characteristics observed in aldose reductase. Although the crystal structure does not include substrate, the two ordered water molecules present within the substrate-binding pocket are postulated to provide positional landmarks for the substrate 5-keto and 4-hydroxyl groups. The structural basis for several previously described active-site mutants of 2,5-DKGR A is also proposed. Recent research efforts have described a novel approach to the synthesis of L-ascorbate (vitamin C) by using a genetically engineered microorganism that is capable of synthesizing 2,5-DKG from glucose and subsequently is transformed with the gene for 2,5-DKGR. These modifications create a microorganism capable of direct production of 2-keto-L-gulonate from D-glucose, and the gulonate can subsequently be converted into vitamin C. In economic terms, vitamin C is the single most important specialty chemical manufactured in the world. Understanding the structural determinants of specificity, catalysis, and stability for 2,5-DKGR A is of substantial commercial interest.

Selected figure(s)

Figure 1.
Fig. 1. Structures of 2,5-diketo-D-gluconate (2,5-DKG), 2-keto-L-gulonate (2-KLG), and L-ascorbate (vitamin C). The uppermost carbon is C1.

Figure 4.
Fig. 4. Noncovalent interactions between the NADPH cofactor and 2,5-DKGR A. In addition to hydrogen bonding and electrostatic interactions, the side chain of Trp-187 is involved in an aromatic stacking interaction with the nicotinamide ring of the NADPH cofactor.

Figures were selected by an automated process.