3FVM

Crystal structure of Steptococcus suis mannonate dehydratase with metal Mn++


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1128/JB.00599-09
  • Primary Citation of Related Structures:  3DBN

  • 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 f ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mannonate dehydratase
A, B
386Streptococcus suis (strain 05ZYH33)Gene Names: uxuA
EC: 4.2.1.8
Find proteins for A4VVI4 (Streptococcus suis (strain 05ZYH33))
Go to UniProtKB:  A4VVI4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.234 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 105.690α = 90.00
b = 105.690β = 90.00
c = 159.572γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance