3CIV

Crystal structure of the endo-beta-1,4-mannanase from Alicyclobacillus acidocaldarius

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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Literature

Biochemical and Structural Characterization of the Intracellular Mannanase AaManA of Alicyclobacillus acidocaldarius Reveals a Novel Glycoside Hydrolase Family Belonging to Clan GH-A

Zhang, Y., Ju, J., Peng, H., Gao, F., Zhou, C., Zeng, Y., Xue, Y., Li, Y., Henrissat, B., Gao, G.F., Ma, Y.

(2008) J Biol Chem 283: 31551-31558

  • DOI: 10.1074/jbc.M803409200
  • Primary Citation of Related Structures:  
    3CIV

  • PubMed Abstract: 

    • An intracellular mannanase was identified from the thermoacidophile Alicyclobacillus acidocaldarius Tc-12-31. This enzyme is particularly interesting, because it shows no significant sequence similarity to any known glycoside hydrolase. Gene cloning, biochemical characterization, and structural studies of this novel mannanase are reported in this paper ...

    An intracellular mannanase was identified from the thermoacidophile Alicyclobacillus acidocaldarius Tc-12-31. This enzyme is particularly interesting, because it shows no significant sequence similarity to any known glycoside hydrolase. Gene cloning, biochemical characterization, and structural studies of this novel mannanase are reported in this paper. The gene consists of 963 bp and encodes a 320-amino acid protein, AaManA. Based on its substrate specificity and product profile, AaManA is classified as an endo-beta-1,4-mannanase that is capable of transglycosylation. Kinetic analysis studies revealed that the enzyme required at least five subsites for efficient hydrolysis. The crystal structure at 1.9 angstroms resolution showed that AaManA adopted a (beta/alpha)8-barrel fold. Two catalytic residues were identified: Glu151 at the C terminus of beta-stand beta4 and Glu231 at the C terminus of beta7. Based on the structure of the enzyme and evidence of its transglycosylation activity, AaManA is placed in clan GH-A. Superpositioning of its structure with that of other clan GH-A enzymes revealed that six of the eight GH-A key residues were functionally conserved in AaManA, with the exceptions being residues Thr95 and Cys150. We propose a model of substrate binding in AaManA in which Glu282 interacts with the axial OH-C(2) in-2 subsites. Based on sequence comparisons, the enzyme was assigned to a new glycoside hydrolase family (GH113) that belongs to clan GH-A.

    Related Citations: 
    • Crystallization and preliminary X-ray study of native and selenomethionyl beta-1,4-mannanase AaManA from Alicyclobacillus acidocaldarius Tc-12-31
      Zhang, Y., Gao, F., Xue, Y., Zeng, Y., Peng, H., Qi, J., Ma, Y.
      (2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 209
    Organizational Affiliation: 

    State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endo-beta-1,4-mannanaseA343Alicyclobacillus acidocaldariusMutation(s): 0 
Gene Names: AamanA
EC: 3.2.1.78
UniProt
Find proteins for A5H1I6 (Alicyclobacillus acidocaldarius)
Explore A5H1I6 
Go to UniProtKB:  A5H1I6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5H1I6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.338α = 90
b = 75.554β = 90
c = 88.016γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance