4CR7 image
Entry Detail
PDB ID:
4CR7
Keywords:
Title:
Crystal structure of the N-acetyl-D-mannosamine dehydrogenase with n-acetylmannosamine
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2014-02-25
Release Date:
2014-07-09
Method Details:
Experimental Method:
Resolution:
2.15 Å
R-Value Free:
0.23
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:N-ACYLMANNOSAMINE 1-DEHYDROGENASE
Chain IDs:A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Chain Length:271
Number of Molecules:16
Biological Source:FLAVOBACTERIUM SP. 141-8
Primary Citation
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)
PMID: 24969681 DOI: 10.1042/BJ20140266

Abstact

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.

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