4COT

The importance of the Abn2 calcium cluster in the endo-1,5- arabinanase activity from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Importance of the Abn2 Calcium Cluster in the Endo-1,5-Arabinanase Activity from Bacillus Subtilis.

Mcvey, C.E.Ferreira, M.J.Correia, B.Lahiri, S.De Sanctis, D.Carrondo, M.A.Lindley, P.F.De Sa Nogueira, I.Soares, C.M.Bento, I.

(2014) J.Biol.Inorg.Chem. 19: 505

  • DOI: 10.1007/s00775-014-1105-x

  • PubMed Abstract: 
  • Arabinanase is a glycosyl hydrolase that is able to cleave the glycosidic bonds of α-1,5-L-arabinan, releasing arabino-oligosaccharides and L-arabinose. The enzyme has two domains, an N-terminal catalytic domain with a characteristic β-propeller fold ...

    Arabinanase is a glycosyl hydrolase that is able to cleave the glycosidic bonds of α-1,5-L-arabinan, releasing arabino-oligosaccharides and L-arabinose. The enzyme has two domains, an N-terminal catalytic domain with a characteristic β-propeller fold and a C-terminal domain whose function is unknown. A calcium ion, located near the catalytic site, serves to stabilize the N-terminal domain, but it has also been proposed to play a key role in the enzyme mechanism. The present work describes the structure of an inactive mutant of the wild-type enzyme (H318Q) and in which the calcium ion has been adventitiously replaced by nickel. These structural studies, together with functional and modelling studies, clearly support the role of the calcium ion in the overall reaction mechanism.


    Organizational Affiliation

    Macromolecular Crystallography Unit, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Protugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXTRACELLULAR ENDO-ALPHA-(1->5)-L-ARABINANASE 2
A
469Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: abn2 (J3A, yxiA)
EC: 3.2.1.99
Find proteins for P42293 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P42293
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.190α = 90.00
b = 76.552β = 112.60
c = 58.073γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
iMOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-03-26
    Type: Atomic model
  • Version 1.2: 2014-06-04
    Type: Database references
  • Version 1.3: 2019-03-06
    Type: Data collection, Experimental preparation, Other