5C6M

Crystal structure of deoxyribose-phosphate aldolase from Shewanella halifaxensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Trading off stability against activity in extremophilic aldolases.

Dick, M.Weiergraber, O.H.Classen, T.Bisterfeld, C.Bramski, J.Gohlke, H.Pietruszka, J.

(2016) Sci Rep 6: 17908-17908

  • DOI: 10.1038/srep17908
  • Primary Citation of Related Structures:  
    5C2X, 5C5Y, 5C6M

  • PubMed Abstract: 
  • Understanding enzyme stability and activity in extremophilic organisms is of great biotechnological interest, but many questions are still unsolved. Using 2-deoxy-D-ribose-5-phosphate aldolase (DERA) as model enzyme, we have evaluated structural and functional characteristics of different orthologs from psychrophilic, mesophilic and hyperthermophilic organisms ...

    Understanding enzyme stability and activity in extremophilic organisms is of great biotechnological interest, but many questions are still unsolved. Using 2-deoxy-D-ribose-5-phosphate aldolase (DERA) as model enzyme, we have evaluated structural and functional characteristics of different orthologs from psychrophilic, mesophilic and hyperthermophilic organisms. We present the first crystal structures of psychrophilic DERAs, revealing a dimeric organization resembling their mesophilic but not their thermophilic counterparts. Conversion into monomeric proteins showed that the native dimer interface contributes to stability only in the hyperthermophilic enzymes. Nevertheless, introduction of a disulfide bridge in the interface of a psychrophilic DERA did confer increased thermostability, suggesting a strategy for rational design of more durable enzyme variants. Constraint network analysis revealed particularly sparse interactions between the substrate pocket and its surrounding α-helices in psychrophilic DERAs, which indicates that a more flexible active center underlies their high turnover numbers.


    Organizational Affiliation

    Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxyribose-phosphate aldolaseA, B, C, D265Shewanella halifaxensisMutation(s): 0 
Gene Names: deoCShal_3136
EC: 4.1.2.4
UniProt
Find proteins for B0TQ91 (Shewanella halifaxensis (strain HAW-EB4))
Explore B0TQ91 
Go to UniProtKB:  B0TQ91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0TQ91
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.03α = 90
b = 52.51β = 122.34
c = 143.21γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release