2YJG

Structure of the lactate racemase apoprotein from Thermoanaerobacterium thermosaccharolyticum

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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This is version 1.2 of the entry. See complete history. 


Literature

Lactate Racemase is a Nickel-Dependent Enzyme Activated by a Widespread Maturation System.

Desguin, B., Goffin, P., Viaene, E., Kleerebezem, M., Martin-Diaconescu, V., Maroney, M.J., Declercq, J., Soumillion, P., Hols, P.

(2014) Nat Commun 5: 3615

  • DOI: 10.1038/ncomms4615
  • Primary Citation of Related Structures:  
    2YJG

  • PubMed Abstract: 

    • Racemases catalyse the inversion of stereochemistry in biological molecules, giving the organism the ability to use both isomers. Among them, lactate racemase remains unexplored due to its intrinsic instability and lack of molecular characterization. Here we determine the genetic basis of lactate racemization in Lactobacillus plantarum ...

    Racemases catalyse the inversion of stereochemistry in biological molecules, giving the organism the ability to use both isomers. Among them, lactate racemase remains unexplored due to its intrinsic instability and lack of molecular characterization. Here we determine the genetic basis of lactate racemization in Lactobacillus plantarum. We show that, unexpectedly, the racemase is a nickel-dependent enzyme with a novel α/β fold. In addition, we decipher the process leading to an active enzyme, which involves the activation of the apo-enzyme by a single nickel-containing maturation protein that requires preactivation by two other accessory proteins. Genomic investigations reveal the wide distribution of the lactate racemase system among prokaryotes, showing the high significance of both lactate enantiomers in carbon metabolism. The even broader distribution of the nickel-based maturation system suggests a function beyond activation of the lactate racemase and possibly linked with other undiscovered nickel-dependent enzymes.

    Organizational Affiliation: 

    1] Institute of Life Sciences, Université catholique de Louvain, Place Croix du Sud 5, 1348 Louvain-La-Neuve, Belgium [2].



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LACTATE RACEMASE APOPROTEINA, B436Thermoanaerobacterium thermosaccharolyticum DSM 571Mutation(s): 0 
Gene Names: larA, Tthe_1662
EC: 5.1.2.1
UniProt
Find proteins for D9TQ02 (Thermoanaerobacterium thermosaccharolyticum (strain ATCC 7956 / DSM 571 / NCIMB 9385 / NCA 3814 / NCTC 13789 / WDCM 00135 / 2032))
Explore D9TQ02 
Go to UniProtKB:  D9TQ02
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9TQ02
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.41α = 90
b = 223.25β = 90
c = 46.14γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other