7PYT

Benzoylsuccinyl-CoA thiolase with coenzyme A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

Starting Model: other
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Finis tolueni: a new type of thiolase with an integrated Zn-finger subunit catalyzes the final step of anaerobic toluene metabolism.

Weidenweber, S.Schuhle, K.Lippert, M.L.Mock, J.Seubert, A.Demmer, U.Ermler, U.Heider, J.

(2022) FEBS J 289: 5599-5616

  • DOI: https://doi.org/10.1111/febs.16443
  • Primary Citation of Related Structures:  
    7PXP, 7PYT, 7YXM

  • PubMed Abstract: 

    Anaerobic toluene degradation involves β-oxidation of the first intermediate (R)-2-benzylsuccinate to succinyl-CoA and benzoyl-CoA. Here, we characterize the last enzyme of this pathway, (S)-2-benzoylsuccinyl-CoA thiolase (BbsAB). Although benzoylsuccinyl-CoA is not available for enzyme assays, the recombinantly produced enzymes from two different species showed the reverse activity, benzoylsuccinyl-CoA formation from benzoyl-CoA and succinyl-CoA. Activity depended on the presence of both subunits, the thiolase family member BbsB and the Zn-finger protein BbsA, which is affiliated to the DUF35 family of unknown function. We determined the structure of BbsAB from Geobacter metallireducens with and without bound CoA at 1.7 and 2.0 Å resolution, respectively. CoA binding into the well-known thiolase cavity triggers an induced-fit movement of the highly disordered covering loop, resulting in its rigidification by forming multiple interactions to the outstretched CoA moiety. This event is coupled with an 8 Å movement of an adjacent hairpin loop of BbsB and the C-terminal domain of BbsA. Thereby, CoA is placed into a catalytically productive conformation, and a putative second CoA binding site involving BbsA and the partner BbsB' subunit is simultaneously formed that also reaches the active center. Therefore, while maintaining the standard thioester-dependent Claisen-type mechanism, BbsAB represents a new type of thiolase.


  • Organizational Affiliation

    Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Benzoylsuccinyl-CoA thiolase subunit
A, C
146Geobacter metallireducens GS-15Mutation(s): 0 
Gene Names: bbsAGmet_1528
UniProt
Find proteins for Q39VG2 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15))
Explore Q39VG2 
Go to UniProtKB:  Q39VG2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39VG2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Benzoylsuccinyl-CoA thiolase subunit
B, D
392Geobacter metallireducens GS-15Mutation(s): 0 
Gene Names: bbsBGmet_1529
UniProt
Find proteins for Q39VG1 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15))
Explore Q39VG1 
Go to UniProtKB:  Q39VG1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39VG1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA (Subject of Investigation/LOI)
Query on COA

Download Ideal Coordinates CCD File 
M [auth D]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
PE8
Query on PE8

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
L [auth C],
O [auth D]
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
P [auth D]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
K [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
N [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.34α = 90
b = 117.34β = 90
c = 228γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySPP1319
German Research Foundation (DFG)GermanySFB-987, He2190/5-1

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Refinement description