Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

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Crystal structures of Streptococcus suis mannonate dehydratase (ManD) and its complex with substrate: genetic and biochemical evidence for a catalytic mechanism

Zhang, Q.Gao, F.Peng, H.Cheng, H.Liu, Y.Tang, J.Thompson, J.Wei, G.Zhang, J.Du, Y.Yan, J.Gao, G.F.

(2009) J Bacteriol 191: 5832-5837

  • DOI: https://doi.org/10.1128/JB.00599-09
  • Primary Citation of Related Structures:  
    3DBN, 3FVM

  • PubMed Abstract: 

    Mannonate dehydratase (ManD) is found only in certain bacterial species, where it participates in the dissimilation of glucuronate. ManD catalyzes the dehydration of d-mannonate to yield 2-keto-3-deoxygluconate (2-KDG), the carbon and energy source for growth. Selective inactivation of ManD by drug targeting is of therapeutic interest in the treatment of human Streptococcus suis infections. Here, we report the overexpression, purification, functional characterization, and crystallographic structure of ManD from S. suis. Importantly, by Fourier transform mass spectrometry, we show that 2-KDG is formed when the chemically synthesized substrate (d-mannonate) is incubated with ManD. Inductively coupled plasma-mass spectrometry revealed the presence of Mn(2+) in the purified protein, and in the solution state catalytically active ManD exists as a homodimer of two 41-kDa subunits. The crystal structures of S. suis ManD in native form and in complex with its substrate and Mn(2+) ion have been solved at a resolution of 2.9 A. The core structure of S. suis ManD is a TIM barrel similar to that of other members of the xylose isomerase-like superfamily. Structural analyses and comparative amino acid sequence alignments provide evidence for the importance of His311 and Tyr325 in ManD activity. The results of site-directed mutagenesis confirmed the functional role(s) of these residues in the dehydration reaction and a plausible mechanism for the ManD-catalyzed reaction is proposed.

  • Organizational Affiliation

    CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mannonate dehydratase
A, B
386Streptococcus suis 05ZYH33Mutation(s): 0 
Gene Names: uxuASSU05_1157
Find proteins for A4VVI4 (Streptococcus suis (strain 05ZYH33))
Explore A4VVI4 
Go to UniProtKB:  A4VVI4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4VVI4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.52α = 90
b = 105.52β = 90
c = 160.077γ = 90
Software Package:
Software NamePurpose

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations