3A72

High resolution structure of Penicillium chrysogenum alpha-L-arabinanase complexed with arabinobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.125 
  • R-Value Observed: 0.104 

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Literature

High-resolution structure of exo-arabinanase from Penicillium chrysogenum

Sogabe, Y.Kitatani, T.Yamaguchi, A.Kinoshita, T.Adachi, H.Takano, K.Inoue, T.Mori, Y.Matsumura, H.Sakamoto, T.Tada, T.

(2011) Acta Crystallogr D Biol Crystallogr 67: 415-422

  • DOI: 10.1107/S0907444911006299
  • Primary Citation of Related Structures:  
    3A71, 3A72

  • PubMed Abstract: 
  • Arabinanase Abnx from Penicillium chrysogenum 31B, which belongs to the GH93 family, releases arabinobiose from the nonreducing terminus of α-1,5-L-arabinan, which is distributed in the primary cell walls of higher plants. Crystal structures of Abnx ...

    Arabinanase Abnx from Penicillium chrysogenum 31B, which belongs to the GH93 family, releases arabinobiose from the nonreducing terminus of α-1,5-L-arabinan, which is distributed in the primary cell walls of higher plants. Crystal structures of Abnx and of its complex with arabinobiose were determined at the high resolutions of 1.14 Å to an R(work) of 10.7% (R(free) = 12.8%) and 1.04 Å to an R(work) of 10.4% (R(free) = 12.5%). Abnx has a six-bladed β-propeller fold with a typical ring-closure mode called `Velcro', in which the last four-stranded β-sheet is completed by the incorporation of a strand from the N-terminus. Catalytic residues which act as a nucleophile and an acid/base were proposed from the structures and confirmed by site-directed mutagenesis. The substrate-binding groove is enclosed at one end by two residues, Glu64 and Tyr66, which contribute to the recognition of the nonreducing chain end of the polysaccharide. A comparison with the related enzyme Arb93A which has a quite similar overall structure suggested that Abnx has different mechanisms to funnel substrates to the active site and/or to stabilize the transition state.


    Organizational Affiliation

    Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exo-arabinanaseA355Penicillium chrysogenumMutation(s): 0 
Gene Names: abnx
EC: 3.2.1.55
Find proteins for Q7ZA77 (Penicillium chrysogenum)
Explore Q7ZA77 
Go to UniProtKB:  Q7ZA77
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose
B
2 N/A Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.125 
  • R-Value Observed: 0.104 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.959α = 90
b = 77.117β = 90
c = 79.574γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-09-11 
  • Released Date: 2010-09-15 
  • Deposition Author(s): Sogabe, Y.

Revision History 

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary