Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 104.95 kDa 
• Atom Count: 7592 
• Modelled Residue Count: 928 
• Deposited Residue Count: 932 
• Unique protein chains: 2

5B46

2-Oxoacid:Ferredoxin Oxidoreductase 2 from Sulfolobus tokodai - ligand free form

• PDB DOI: 10.2210/pdb5B46/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-01 Released: 2016-09-28 
• Deposition Author(s): Yan, Z., Maruyama, A., Arakawa, T., Fushinobu, S., Wakagi, T.
• Funding Organization(s): JSPS KAKENHI

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.219 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Crystal structures of archaeal 2-oxoacid:ferredoxin oxidoreductases from Sulfolobus tokodaii

Yan, Z., Maruyama, A., Arakawa, T., Fushinobu, S., Wakagi, T.

(2016) Sci Rep 6: 33061-33061

• PubMed: 27619895 
• DOI: 10.1038/srep33061
• Primary Citation of Related Structures:  
  5B46, 5B47, 5B48


• PubMed Abstract: 
  

As the first three-dimensional structure of the two-subunit type 2-oxoacid:ferredoxin oxidoreductases (OFOR) from archaea, we solved the crystal structures of STK_23000/STK_22980 (StOFOR1) and STK_24350/STK_24330 (StOFOR2) from Sulfolobus tokodaii. They showed similar overall structures, consisting of two a- and b-subunit heterodimers containing thiamin pyrophosphate (TPP) cofactor and [4Fe-4S] cluster, but lack an intramolecular ferredoxin domain. Unlike other OFORs, StOFORs can utilize both pyruvate and 2-oxoglutarate, playing a key role in the central metabolism. In the structure of StOFOR2 in unreacted pyruvate complex form, carboxylate group of pyruvate is recognized by Arg344 and Thr257 from the a-subunit, which are conserved in pyruvate:ferredoxin oxidoreductase from Desulfovbrio africanus (DaPFOR). In the structure of StOFOR1 co-crystallized with 2-oxobutyrate, electron density corresponding to a 1-hydroxypropyl group (post-decarboxylation state) was observed at the thiazole ring of TPP. The binding pockets of the StOFORs surrounding the methyl or propyl group of the ligands are wider than that of DaPFOR. Mutational analyses indicated that several residues were responsible for the broad 2-oxoacid specificity of StOFORs. We also constructed a possible complex structural model by placing a Zn(2+)-containing dicluster ferredoxin of S. tokodaii into the large pocket of StOFOR2, providing insight into the electron transfer between the two redox proteins.

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Organizational Affiliation: 

Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxoacid--ferredoxin oxidoreductase alpha subunit	A	628	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  Gene Names: STK_24350, ST2435 EC: 1.2.7 (PDB Primary Data), 1.2.7.11 (UniProt)
UniProt
Find proteins for Q96XT2 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q96XT2  Go to UniProtKB:  Q96XT2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxoacid--ferredoxin oxidoreductase beta subunit	B	304	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  Gene Names: STK_24330, ST2433 EC: 1.2.7 (PDB Primary Data), 1.2.7.11 (UniProt)
UniProt
Find proteins for Q96XT4 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q96XT4  Go to UniProtKB:  Q96XT4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	D [auth B]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
SF4	C [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
MG	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.219 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.889	α = 90
b = 205.048	β = 90
c = 126.988	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-04-01 
• Released Date: 2016-09-28 
Deposition Author(s): Yan, Z., Maruyama, A., Arakawa, T., Fushinobu, S., Wakagi, T.

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Funding Organization	Location	Grant Number
JSPS KAKENHI	Japan	24580136

Revision History  

• Version 1.0: 2016-09-28
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection, Derived calculations