PDBsum entry: 1nxu

Structural genomics, oxidoreductase

PDB id: 1nxu

Contents

Protein chains

332 a.a. *

Ligands

SO4 ×4

Waters ×664

* Residue conservation analysis

PDB id:

1nxu

Name:

Structural genomics, oxidoreductase

Title:

Crystal structure of e. Coli hypothetical oxidoreductase yiak northeast structural genomics consortium target er82.

Structure:

Hypothetical oxidoreductase yiak. Chain: a, b. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: yiak or b3575. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.192 R-free: 0.235

Authors:

F.Forouhar,I.Lee,J.Benach,K.Kulkarni,R.Xiao,T.B.Acton, R.Shastry,B.Rost,G.T.Montelione,L.Tong,Northeast Structural Genomics Consortium (Nesg)

Key ref:

F.Forouhar et al. (2004). A novel NAD-binding protein revealed by the crystal structure of 2,3-diketo-L-gulonate reductase (YiaK). J Biol Chem, 279, 13148-13155. PubMed id: 14718529 DOI: 10.1074/jbc.M313580200

Date:

11-Feb-03 Release date: 11-Mar-03

Protein chains

P37672  (DLGD_ECOLI) -  2,3-diketo-L-gulonate reductase

Seq: 332 a.a.

Struc: 332 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.130 - 3-dehydro-L-gulonate 2-dehydrogenase.
• Reaction: 3-dehydro-L-gulonate + NAD(P)(+) = (4R,5S)-4,5,6-trihydroxy-2,3- dioxohexanoate + NAD(P)H

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: metabolic process (2 terms)
• Biochemical function: oxidoreductase activity (3 terms)

reference

DOI no: 10.1074/jbc.M313580200

J Biol Chem 279:13148-13155 (2004)

PubMed id: 14718529

A novel NAD-binding protein revealed by the crystal structure of 2,3-diketo-L-gulonate reductase (YiaK).

F.Forouhar, I.Lee, J.Benach, K.Kulkarni, R.Xiao, T.B.Acton, G.T.Montelione, L.Tong.

ABSTRACT

Escherichia coli YiaK catalyzes the reduction of 2,3-diketo-L-gulonate in the presence of NADH. It belongs to a large family of oxidoreductases that is conserved in archaea, bacteria, and eukaryotes but shows no sequence homology to other proteins. We report here the crystal structures at up to 2.0-A resolution of YiaK alone and in complex with NAD-tartrate. YiaK has a new polypeptide backbone fold and a novel mode of recognizing the NAD cofactor. In addition, NAD is bound in an unusual conformation, at the interface of a dimer of the enzyme. The crystallographic analysis unexpectedly revealed the binding of tartrate in the active site. Enzyme kinetics studies confirm that tartrate and the related D-malate are inhibitors of YiaK. In contrast to most other enzymes where substrate binding produces a more closed conformation, the binding of NAD-tartrate to YiaK produces a more open active site. The free enzyme conformation is incompatible with NAD binding. His(44) is likely the catalytic residue of the enzyme.

Selected figure(s)

Figure 4.
FIG. 4. The binding mode of tartrate. A, final 2F[o] - F[c] electron density at a 2.2-Å resolution for the tartrate molecule bound to monomer A, contoured at 1 . B, molecular surface of the active-site region of YiaK. The tartrate molecule is shown as a stick model in green. C, stereographic drawing of the interactions between tartrate and YiaK. Hydrogen-bonding interactions are indicated by the dashed lines. A was created with SETOR (24), B was created with GRASP (22), and C was created with Molscript (25) and Raster3D (26).

Figure 5.
FIG. 5. Conformational change in YiaK upon NAD binding. A, structural overlay of the monomers of the free enzyme (magenta) and the NAD-tartrate complex (yellow) of YiaK. B, molecular surface of the active-site region of YiaK in the free enzyme structure. The NAD and tartrate molecules as observed in the complex structure are shown for reference. C, the active site of the free enzyme structure. The two sulfate ions (SO[4]) bound in the active site are shown. The NAD-tartrate molecules are shown for reference. TAR, tartrate; arrows, point to the sulfate ions. A and C were created with Molscript (25) and Raster3D (26), and B was created with GRASP (22).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 13148-13155) copyright 2004.

Figures were selected by an automated process.