3H8I

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

PDB DOI: https://doi.org/10.2210/pdb3H8I/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.225
R-Value Work: 0.196
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1021/bi9003827
Primary Citation of 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 92.97 kDa
Atom Count: 5,916
Modelled Residue Count: 712
Deposited Residue Count: 818
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt
Find proteins for Q7ZAG8 (Acidianus ambivalens) Explore Q7ZAG8 Go to UniProtKB: Q7ZAG8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7ZAG8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B]	C [auth A], J [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
S3H Query on S3H Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B]	D [auth A], K [auth B]	trisulfane H₂ S₃ KBMBVTRWEAAZEY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth B] 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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]