2GUY

Orthorhombic crystal structure (space group P21212) of Aspergillus niger alpha-amylase at 1.6 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 angstroms resolution.

Vujicic-Zagar, A.Dijkstra, B.W.

(2006) Acta Crystallogr.,Sect.F 62: 716-721

  • DOI: 10.1107/S1744309106024729
  • Primary Citation of Related Structures:  2GVY

  • PubMed Abstract: 
  • Aspergillus niger alpha-amylase catalyses the hydrolysis of alpha-1,4-glucosidic bonds in starch. It shows 100% sequence identity to the A. oryzae homologue (also called TAKA-amylase), three crystal structures of which have been published to date. Tw ...

    Aspergillus niger alpha-amylase catalyses the hydrolysis of alpha-1,4-glucosidic bonds in starch. It shows 100% sequence identity to the A. oryzae homologue (also called TAKA-amylase), three crystal structures of which have been published to date. Two of them belong to the orthorhombic space group P2(1)2(1)2(1) with one molecule per asymmetric unit and one belongs to the monoclinic space group P2(1) with three molecules per asymmetric unit. Here, the purification, crystallization and structure determination of A. niger alpha-amylase crystallized in the monoclinic space group P2(1) with two molecules per asymmetric unit in complex with maltose at 1.8 angstroms resolution is reported. Furthermore, a novel 1.6 angstroms resolution orthorhombic crystal form (space group P2(1)2(1)2) of the native enzyme is presented. Four maltose molecules are observed in the maltose-alpha-amylase complex. Three of these occupy active-site subsites -2 and -1, +1 and +2 and the hitherto unobserved subsites +4 (Asp233, Gly234) and +5 (Asp235). The fourth maltose molecule binds at the distant binding sites d1 (Tyr382) and d2 (Trp385), also previously unobserved. Furthermore, it is shown that the active-site groove permits different binding modes of sugar units at subsites +1 and +2. This flexibility of the active-site cleft close to the catalytic centre might be needed for a productive binding of substrate chains and/or release of products.


    Organizational Affiliation

    Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-amylase A
A
478Aspergillus oryzae (strain ATCC 42149 / RIB 40)Gene Names: amy1, amy2 (amyI, Taa-G1, amyII, Taa-G2)
EC: 3.2.1.1
Find proteins for P0C1B3 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Go to UniProtKB:  P0C1B3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 102.799α = 90.00
b = 63.228β = 90.00
c = 74.456γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
ProDCdata collection
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-05-02 
  • Released Date: 2006-08-15 
  • Deposition Author(s): Vujicic Zagar, A.

Revision History 

  • Version 1.0: 2006-08-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description