3A71

High resolution structure of Penicillium chrysogenum alpha-L-arabinanase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

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.,Sect.D 67: 415-422

  • DOI: 10.1107/S0907444911006299
  • Primary Citation of Related Structures:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exo-arabinanase
A
355Penicillium chrysogenumMutation(s): 0 
Gene Names: abnx
Find proteins for Q7ZA77 (Penicillium chrysogenum)
Go to UniProtKB:  Q7ZA77
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT
Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MPD
Query on MPD
Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.128 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.877α = 90.00
b = 77.248β = 90.00
c = 79.441γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLVEphasing
SHELXL-97refinement
HKL-2000data collection
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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
    Type: Version format compliance