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 
  • R-Value Observed: 0.107 

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 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 and of its complex with arabinobiose were determined at the high resolutions of 1 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exo-arabinanaseA355Penicillium chrysogenumMutation(s): 0 
Gene Names: abnx
EC: 3.2.1.55
UniProt
Find proteins for Q7ZA77 (Penicillium chrysogenum)
Explore Q7ZA77 
Go to UniProtKB:  Q7ZA77
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7ZA77
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.128 
  • R-Value Observed: 0.107 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.877α = 90
b = 77.248β = 90
c = 79.441γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
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  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance