4COT | pdb_00004cot

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: 1.90 Å
  • R-Value Free: 
    0.214 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1007/s00775-014-1105-x
  • Primary Citation Related Structures: 
    4COT

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 52.84 kDa 
  • Atom Count: 3,822 
  • Modeled Residue Count: 443 
  • Deposited Residue Count: 469 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
EXTRACELLULAR ENDO-ALPHA-(1->5)-L-ARABINANASE 2469Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
EC: 3.2.1.99
UniProt
Find proteins for P42293 (Bacillus subtilis (strain 168))
Explore P42293 
Go to UniProtKB:  P42293
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42293
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.214 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.19α = 90
b = 76.552β = 112.6
c = 58.073γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-03-26
    Changes: Atomic model
  • Version 1.2: 2014-06-04
    Changes: Database references
  • Version 1.3: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description