4CR6

Crystal structure of the N-acetyl-D-mannosamine dehydrogenase without substrates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal Structures and Functional Studies Clarify Substrate Selectivity and Catalytic Residues for the Unique Orphan Enzyme N-Acetyl-D-Mannosamine Dehydrogenase.

Sola-Carvajal, A.Gil-Ortiz, F.Garcia-Carmona, F.Rubio, V.Sanchez-Ferrer, A.

(2014) Biochem J 462: 499

  • DOI: https://doi.org/10.1042/BJ20140266
  • Primary Citation of Related Structures:  
    4CR6, 4CR7, 4CR8

  • 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.


  • Organizational Affiliation

    *Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, Campus Espinardo, E-30100 Murcia, Spain.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-ACYLMANNOSAMINE 1-DEHYDROGENASE
A, B, C, D
271Flavobacterium sp. 141-8Mutation(s): 0 
EC: 1.1.1.233
UniProt
Find proteins for P22441 (Flavobacterium sp. (strain 141-8))
Explore P22441 
Go to UniProtKB:  P22441
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22441
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.255α = 81.13
b = 59.062β = 73.29
c = 74.206γ = 79.25
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-09-03
    Changes: Database references, Other
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary