6Y0K

Sulfite oxidase from Thermus thermophilus with coordinated phosphate

• PDB DOI: https://doi.org/10.2210/pdb6Y0K/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2020-02-08 Released: 2020-08-05 
• Deposition Author(s): Djeghader, A., Soulimane, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.191 
• R-Value Work: 0.166 

Literature

Structural evidence for a reaction intermediate mimic in the active site of a sulfite dehydrogenase.

Djeghader, A., Rossotti, M., Abdulkarim, S., Biaso, F., Gerbaud, G., Nitschke, W., Schoepp-Cothenet, B., Soulimane, T., Grimaldi, S.

(2020) Chem Commun (Camb) 56: 9850-9853

• PubMed: 32716419 
• DOI: https://doi.org/10.1039/d0cc03634j
• Primary Citation of Related Structures:  
  6Y0K


• PubMed Abstract: 
  

  By combining X-ray crystallography, electron paramagnetic resonance techniques and density functional theory-based modelling, we provide evidence for a direct coordination of the product analogue, phosphate, to the molybdenum active site of a sulfite dehydrogenase. This interaction is mimicking the still experimentally uncharacterized reaction intermediate proposed to arise during the catalytic cycle of this class of enzymes. This work opens new perspectives for further deciphering the reaction mechanism of this nearly ubiquitous class of oxidoreductases.

---

Organizational Affiliation: 

Department of Chemical Sciences and Bernal Institute, University of Limerick, Ireland. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 44.41 kDa 
• Atom Count: 3,485 
• Modelled Residue Count: 377 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putaitve sulfite oxidase	A [auth AAA]	386	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA1325
UniProt
Find proteins for Q5SIP4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIP4  Go to UniProtKB:  Q5SIP4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MSS (Subject of Investigation/LOI)	B [auth AAA]	(MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM C10 H12 Mo N5 O7 P S2 BDXDYZBRBRKVRM-MRZGRPIRSA-L
PO4	F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth AAA], D [auth AAA], E [auth AAA], J [auth AAA]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.191 
• R-Value Work: 0.166 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.6	α = 90
b = 130.6	β = 90
c = 114.59	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Djeghader, A., Soulimane, T.

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2020-08-12
  Changes: Database references
• Version 1.2: 2020-09-02
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description