9PZJ | pdb_00009pzj

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.246 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Accessory Subunit Regulates Thiyl Radical Formation in Benzylsuccinate Synthase.

Anas, S.Liu, J.Vats, A.Gainadi, R.Sharif, S.Piriyatamwong, A.Andorfer, M.C.

(2025) Biochemistry 64: 4414-4423

  • DOI: https://doi.org/10.1021/acs.biochem.5c00492
  • Primary Citation of Related Structures:  
    9PZJ

  • PubMed Abstract: 

    X-succinate synthases (XSSs) are a class of glycyl radical enzymes (GREs) that enable anaerobic hydrocarbon functionalization, granting anaerobes access to petroleum-derived substrates for metabolism. Owing to their ability to functionalize components of crude oil and catalyze selective olefin hydroalkylation, XSSs hold significant biotechnological promise. However, mechanistic understanding has been limited due to long-standing barriers to installing their essential glycyl radical in vitro, which have only recently been overcome. Unlike most GREs, XSSs contain accessory subunits that bind to the periphery of the catalytic subunit. The most well-studied XSS, benzylsuccinate synthase (BSS), includes two [4Fe-4S] cluster-binding accessory subunits, BSSγ and BSSβ. The full structure of BSSγ and the catalytic role of BSSβ have remained unclear. Here, we report the crystal structure of BSSγ with its [4Fe-4S] cluster intact, revealing a HiPP-like fold similar to that of BSSβ. Through biochemical and spectroscopic studies, we provide evidence that BSSβ promotes thiyl radical formation, even in the absence of a substrate. This finding contrasts with recent models, in which substrate binding is required to trigger thiyl radical formation. With this mechanistic insight, we optimized reaction conditions to achieve total turnover numbers of ∼17,000, representing an over 340-fold improvement compared to prior reports. We further show that in the absence of BSSβ, activated BSSαγ remains catalytically active for up to 11 days. Together, these results clarify the unique regulatory architecture of BSS and lay the groundwork for the use of XSSs in biocatalytic applications.


  • Organizational Affiliation
    • Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
benzylsuccinate synthase alpha chain
A, D
878Thauera 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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68395
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
benzylsuccinate synthase beta chain
B, E
102Thauera aromaticaMutation(s): 0 
Gene Names: tutG
UniProt
Find proteins for O68396 (Thauera aromatica)
Explore O68396 
Go to UniProtKB:  O68396
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68396
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
benzylsuccinate synthase gamma chain
C, F
60Thauera aromaticaMutation(s): 0 
Gene Names: tutF
UniProt
Find proteins for O68394 (Thauera aromatica)
Explore O68394 
Go to UniProtKB:  O68394
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68394
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
J [auth B],
K [auth C],
O [auth E],
P [auth F]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FUM (Subject of Investigation/LOI)
Query on FUM

Download Ideal Coordinates CCD File 
G [auth A],
L [auth D]
FUMARIC ACID
C4 H4 O4
VZCYOOQTPOCHFL-OWOJBTEDSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A],
N [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MBN (Subject of Investigation/LOI)
Query on MBN

Download Ideal Coordinates CCD File 
H [auth A],
M [auth D]
TOLUENE
C7 H8
YXFVVABEGXRONW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.396α = 90
b = 118.535β = 90
c = 124.929γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM145910

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Database references