4CR8

Crystal structure of the N-acetyl-D-mannosamine dehydrogenase with NAD

Summary for 4CR8

• Entry DOI: 10.2210/pdb4cr8/pdb
• Related: 4CR6 4CR7
• Descriptor: N-ACYLMANNOSAMINE 1-DEHYDROGENASE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE (3 entities in total)
• Functional Keywords: oxidoreductase, short-chain dehydrogenase/reductase, substrate selectivity
• Biological source: FLAVOBACTERIUM SP. 141-8
• Total number of polymer chains: 8
• Total formula weight: 225270.17

Authors

Gil-Ortiz, F.,Sola-Carvajal, A.,Garcia-Carmona, F.,Sanchez-Ferrer, A.,Rubio, V. (deposition date: 2014-02-25, release date: 2014-07-09, Last modification date: 2023-12-20)

Primary citation

Sola-Carvajal, A.,Gil-Ortiz, F.,Garcia-Carmona, F.,Rubio, V.,Sanchez-Ferrer, A.
Crystal Structures and Functional Studies Clarify Substrate Selectivity and Catalytic Residues for the Unique Orphan Enzyme N-Acetyl-D-Mannosamine Dehydrogenase.
Biochem.J., 462:499-, 2014

PubMed Abstract: NAMDH (N-acetyl-D-mannosamine dehydrogenase), from the soil bacteroidete Flavobacterium sp. 141-8, catalyses a rare NAD+-dependent oxidation of ManNAc (N-acetyl-D-mannosamine) into N-acetylmannosamino-lactone, which spontaneously hydrolyses into N-acetylmannosaminic acid. NAMDH belongs to the SDR (short-chain dehydrogenase/reductase) superfamily and is the only NAMDH characterized to date. Thorough functional, stability, site-directed mutagenesis and crystallographic studies have been carried out to understand better the structural and biochemical aspects of this unique enzyme. NAMDH exhibited a remarkable alkaline pH optimum (pH 9.4) with a high thermal stability in glycine buffer (Tm=64°C) and a strict selectivity towards ManNAc and NAD+. Crystal structures of ligand-free and ManNAc- and NAD+-bound enzyme forms revealed a compact homotetramer having point 222 symmetry, formed by subunits presenting the characteristic SDR α3β7α3 sandwich fold. A highly developed C-terminal tail used as a latch connecting nearby subunits stabilizes the tetramer. A dense network of polar interactions with the substrate including the encasement of its acetamido group in a specific binding pocket and the hydrogen binding of the sugar 4OH atom ensure specificity for ManNAc. The NAMDH-substrate complexes and site-directed mutagenesis studies identify the catalytic tetrad and provide useful traits for identifying new NAMDH sequences.

PubMed: 24969681
DOI: 10.1042/BJ20140266

Experimental method

X-RAY DIFFRACTION (2.2 Å)