5BWE

Benzylsuccinate synthase alpha-beta-gamma complex with bound toluene and fumarate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Substrate-bound Structures of Benzylsuccinate Synthase Reveal How Toluene Is Activated in Anaerobic Hydrocarbon Degradation.

Funk, M.A.Marsh, E.N.Drennan, C.L.

(2015) J Biol Chem 290: 22398-22408

  • DOI: 10.1074/jbc.M115.670737
  • Primary Citation of Related Structures:  
    5BWD, 5BWE

  • PubMed Abstract: 
  • Various bacteria perform anaerobic degradation of small hydrocarbons as a source of energy and cellular carbon. To activate non-reactive hydrocarbons such as toluene, enzymes conjugate these molecules to fumarate in a radical-catalyzed, C-C bond-forming reaction ...

    Various bacteria perform anaerobic degradation of small hydrocarbons as a source of energy and cellular carbon. To activate non-reactive hydrocarbons such as toluene, enzymes conjugate these molecules to fumarate in a radical-catalyzed, C-C bond-forming reaction. We have determined x-ray crystal structures of the glycyl radical enzyme that catalyzes the addition of toluene to fumarate, benzylsuccinate synthase (BSS), in two oligomeric states with fumarate alone or with both substrates. We find that fumarate is secured at the bottom of a long active site cavity with toluene bound directly above it. The two substrates adopt orientations that appear ideal for radical-mediated C-C bond formation; the methyl group of toluene is positioned between fumarate and a cysteine that forms a thiyl radical during catalysis, which is in turn adjacent to the glycine that serves as a radical storage residue. Toluene is held in place by fumarate on one face and tight packing by hydrophobic residues on the other face and sides. These hydrophobic residues appear to become ordered, thus encapsulating toluene, only in the presence of BSSβ, a small protein subunit that forms a tight complex with BSSα, the catalytic subunit. Enzymes related to BSS are able to metabolize a wide range of hydrocarbons through attachment to fumarate. Using our structures as a guide, we have constructed homology models of several of these "X-succinate synthases" and determined conservation patterns that will be useful in understanding the basis for catalysis and specificity in this family of enzymes.


    Organizational Affiliation

    From the Departments of Chemistry and Biology and the Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and cdrennan@mit.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
benzylsuccinate synthase alpha chainA, D878Thauera aromaticaMutation(s): 1 
Gene Names: tutD
EC: 4.1.99.11
UniProt
Find proteins for O68395 (Thauera aromatica)
Explore O68395 
Go to UniProtKB:  O68395
Entity Groups  
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UniProt GroupO68395
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
benzylsuccinate synthase beta chainB,
E [auth F]
81Thauera aromaticaMutation(s): 0 
Gene Names: tutG
UniProt
Find proteins for O68396 (Thauera aromatica)
Explore O68396 
Go to UniProtKB:  O68396
Entity Groups  
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UniProt GroupO68396
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
benzylsuccinate synthase gamma chainC,
F [auth G]
60Thauera aromaticaMutation(s): 0 
Gene Names: tutF
UniProt
Find proteins for O68394 (Thauera aromatica)
Explore O68394 
Go to UniProtKB:  O68394
Entity Groups  
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UniProt GroupO68394
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 2
  • Diffraction Data DOI: 10.15785/SBGRID/147
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.534α = 90
b = 115.36β = 90
c = 121.701γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States0645960
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2015-09-23
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence