2E1M

Crystal Structure of L-Glutamate Oxidase from Streptomyces sp. X-119-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

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This is version 1.1 of the entry. See complete history


Literature

Structural characterization of l-glutamate oxidase from Streptomyces sp. X-119-6

Arima, J.Sasaki, C.Sakaguchi, C.Mizuno, H.Tamura, T.Kashima, A.Kusakabe, H.Sugio, S.Inagaki, K.

(2009) FEBS J 276: 4318-4327

  • DOI: 10.1111/j.1742-4658.2009.07103.x
  • Primary Citation of Related Structures:  
    2E1M

  • PubMed Abstract: 
  • L-Glutamate oxidase (LGOX) from Streptomyces sp. X-119-6, which catalyzes the oxidative deamination of L-glutamate, has attracted increasing attention as a component of amperometric L-glutamate sensors used in the food industry and clinical biochemistry. The precursor of LGOX, which has a homodimeric structure, is less active than the mature enzyme with an alpha(2)beta(2)V(2) structure; enzymatic proteolysis of the precursor forms the stable mature enzyme ...

    L-Glutamate oxidase (LGOX) from Streptomyces sp. X-119-6, which catalyzes the oxidative deamination of L-glutamate, has attracted increasing attention as a component of amperometric L-glutamate sensors used in the food industry and clinical biochemistry. The precursor of LGOX, which has a homodimeric structure, is less active than the mature enzyme with an alpha(2)beta(2)V(2) structure; enzymatic proteolysis of the precursor forms the stable mature enzyme. We solved the crystal structure of mature LGOX using molecular replacement with a structurally homologous model of L-amino acid oxidase (LAAO) from snake venom: LGOX has a deeply buried active site and two entrances from the surface of the protein into the active site. Comparison of the LGOX structure with that of LAAO revealed that LGOX has three regions that are absent from the LAAO structure, one of which is involved in the formation of the entrance. Furthermore, the arrangement of the residues composing the active site differs between LGOX and LAAO, and the active site of LGOX is narrower than that of LAAO. Results of the comparative analyses described herein raise the possibility that such a unique structure of LGOX is associated with its substrate specificity.


    Organizational Affiliation

    Department of Biofunctional Chemistry, Graduate School of Natural Science and Technology, Okayama University, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-glutamate oxidaseA376Streptomyces sp. X-119-6Mutation(s): 0 
Gene Names: Lgox
EC: 1.4.3.11
UniProt
Find proteins for Q8L3C7 (Streptomyces sp. X-119-6)
Explore Q8L3C7 
Go to UniProtKB:  Q8L3C7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8L3C7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
L-glutamate oxidaseB130Streptomyces sp. X-119-6Mutation(s): 0 
Gene Names: Lgox
EC: 1.4.3.11
UniProt
Find proteins for Q8L3C7 (Streptomyces sp. X-119-6)
Explore Q8L3C7 
Go to UniProtKB:  Q8L3C7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8L3C7
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
L-glutamate oxidaseC181Streptomyces sp. X-119-6Mutation(s): 0 
Gene Names: Lgox
EC: 1.4.3.11
UniProt
Find proteins for Q8L3C7 (Streptomyces sp. X-119-6)
Explore Q8L3C7 
Go to UniProtKB:  Q8L3C7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8L3C7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
G [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.875α = 90
b = 123.875β = 90
c = 168.762γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance