1S20

A novel NAD binding protein revealed by the crystal structure of E. Coli 2,3-diketogulonate reductase (YiaK) NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82

Summary for 1S20

• Entry DOI: 10.2210/pdb1s20/pdb
• Related: 1NXU
• Descriptor: Hypothetical oxidoreductase yiaK, L(+)-TARTARIC ACID, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (4 entities in total)
• Functional Keywords: alpha beta dimeric protein, oxidoreductase, structural genomics, psi-2, protein structure initiative, northeast structural genomics consortium, nesg
• Biological source: Escherichia coli
• Cellular location: Cytoplasm (Potential): P37672
• Total number of polymer chains: 8
• Total formula weight: 311962.73

Authors

Forouhar, F.,Lee, I.,Benach, J.,Kulkarni, K.,Xiao, R.,Acton, T.B.,Montelione, G.T.,Tong, L.,Northeast Structural Genomics Consortium (NESG) (deposition date: 2004-01-07, release date: 2004-01-20, Last modification date: 2023-11-15)

Primary citation

Forouhar, F.,Lee, I.,Benach, J.,Kulkarni, K.,Xiao, R.,Acton, T.B.,Montelione, G.T.,Tong, L.
A Novel NAD-binding Protein Revealed by the Crystal Structure of 2,3-Diketo-L-gulonate Reductase (YiaK).
J.Biol.Chem., 279:13148-13155, 2004

PubMed 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.

PubMed: 14718529
DOI: 10.1074/jbc.M313580200

Experimental method

X-RAY DIFFRACTION (2.2 Å)