3H8L | pdb_00003h8l

The first X-ray structure of a sulfide:quinone oxidoreductase: insights into sulfide oxidation mechanism

• PDB DOI: https://doi.org/10.2210/pdb3H8L/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acidianus ambivalens
• Mutation(s): No 


• Deposited: 2009-04-29 Released: 2009-06-02 
• Deposition Author(s): Brito, J.A., Sousa, F.L., Stelter, M., Bandeiras, T.M., Vonrhein, C., Teixeira, M., Pereira, M.M., Archer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 
  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Structural and functional insights into sulfide:quinone oxidoreductase.

Brito, J.A., Sousa, F.L., Stelter, M., Bandeiras, T.M., Vonrhein, C., Teixeira, M., Pereira, M.M., Archer, M.

(2009) Biochemistry 48: 5613-5622

• PubMed: 19438211 
• DOI: https://doi.org/10.1021/bi9003827
• Primary Citation Related Structures: 
  3H8I, 3H8L


• PubMed Abstract: 
  

  A sulfide:quinone oxidoreductase (SQR) was isolated from the membranes of the hyperthermoacidophilic archaeon Acidianus ambivalens, and its X-ray structure, the first reported for an SQR, was determined to 2.6 A resolution. This enzyme was functionally and structurally characterized and was shown to have two redox active sites: a covalently bound FAD and an adjacent pair of cysteine residues. Most interestingly, the X-ray structure revealed the presence of a chain of three sulfur atoms bridging those two cysteine residues. The possible implications of this observation in the catalytic mechanism for sulfide oxidation are discussed, and the role of SQR in the sulfur dependent bioenergetics of A. ambivalens, linked to oxygen reduction, is addressed.

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Organizational Affiliation: 
• Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal.

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)

Macromolecule Content 

• Total Structure Weight: 92.97 kDa 
• Atom Count: 6,014 
• Modeled Residue Count: 712 
• Deposited Residue Count: 818 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH oxidase	A, B	409	Acidianus ambivalens	Mutation(s): 0  EC: 1.6.99.3 (PDB Primary Data), 1.8.5.4 (UniProt)
UniProt
Find proteins for Q7ZAG8 (Acidianus ambivalens) Explore Q7ZAG8  Go to UniProtKB:  Q7ZAG8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], J [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
S3H	D [auth A], K [auth B]	trisulfane H2 S3 KBMBVTRWEAAZEY-UHFFFAOYSA-N
PO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.657	α = 90
b = 179.657	β = 90
c = 163.397	γ = 120

Software Package:

Software Name	Purpose
DNA	data collection
SHARP	phasing
BUSTER-TNT	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-02 
Deposition Author(s): Brito, J.A., Sousa, F.L., Stelter, M., Bandeiras, T.M., Vonrhein, C., Teixeira, M., Pereira, M.M., Archer, M.

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary