7PCS

Structure of the heterotetrameric SDR family member BbsCD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


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Literature

Inactive pseudoenzyme subunits in heterotetrameric BbsCD, a novel short-chain alcohol dehydrogenase involved in anaerobic toluene degradation.

von Horsten, S.Lippert, M.L.Geisselbrecht, Y.Schuhle, K.Schall, I.Essen, L.O.Heider, J.

(2022) FEBS J 289: 1023-1042

  • DOI: https://doi.org/10.1111/febs.16216
  • Primary Citation of Related Structures:  
    7PCS

  • PubMed Abstract: 

    Anaerobic toluene degradation proceeds by fumarate addition to produce (R)-benzylsuccinate as first intermediate, which is further degraded via β-oxidation by five enzymes encoded in the conserved bbs operon. This study characterizes two enzymes of this pathway, (E)-benzylidenesuccinyl-CoA hydratase (BbsH), and (S,R)-2-(α-hydroxybenzyl)succinyl-CoA dehydrogenase (BbsCD) from Thauera aromatica. BbsH, a member of the enoyl-CoA hydratase family, converts (E)-benzylidenesuccinyl-CoA to 2-(α-hydroxybenzyl)succinyl-CoA and was subsequently used in a coupled enzyme assay with BbsCD, which belongs to the short-chain dehydrogenases/reductase (SDR) family. The BbsCD crystal structure shows a C2-symmetric heterotetramer consisting of BbsC 2 and BbsD 2 dimers. BbsD subunits are catalytically active and capable of binding NAD + and substrate, whereas BbsC subunits represent built-in pseudoenzyme moieties lacking all motifs of the SDR family required for substrate binding or catalysis. Molecular modeling studies predict that the active site of BbsD is specific for conversion of the (S,R)-diastereomer of 2-(α-hydroxybenzyl)succinyl-CoA to (S)-2-benzoylsuccinyl-CoA by hydride transfer to the re-face of nicotinamide adenine dinucleotide (NAD) + . Furthermore, BbsC subunits are not engaged in substrate binding and merely serve as scaffold for the BbsD dimer. BbsCD represents a novel clade of related enzymes within the SDR family, which adopt a heterotetrameric architecture and catalyze the β-oxidation of aromatic succinate adducts.


  • Organizational Affiliation

    Department of Biology, Philipps-Universität, Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BbsC
A, C
250Thauera aromaticaMutation(s): 1 
Gene Names: bbsC
UniProt
Find proteins for Q9KJF2 (Thauera aromatica)
Explore Q9KJF2 
Go to UniProtKB:  Q9KJF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KJF2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BbsD
B, D
248Thauera aromaticaMutation(s): 0 
Gene Names: bbsD
UniProt
Find proteins for Q9KJF1 (Thauera aromatica)
Explore Q9KJF1 
Go to UniProtKB:  Q9KJF1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KJF1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
G [auth B],
K [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth C]
J [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth C],
J [auth C],
L [auth D],
M [auth D],
N [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.6α = 90
b = 68.6β = 90
c = 191.96γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
SHELXCDphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB987

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release