1T3Q | pdb_00001t3q

Crystal structure of quinoline 2-Oxidoreductase from Pseudomonas Putida 86

• PDB DOI: https://doi.org/10.2210/pdb1T3Q/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Mutation(s): No 


• Deposited: 2004-04-27 Released: 2004-09-14 
• Deposition Author(s): Bonin, I., Martins, B.M., Purvanov, V., Fetzner, S., Huber, R., Dobbek, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.207 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Active site geometry and substrate recognition of the molybdenum hydroxylase quinoline 2-oxidoreductase.

Bonin, I., Martins, B.M., Purvanov, V., Fetzner, S., Huber, R., Dobbek, H.

(2004) Structure 12: 1425-1435

• PubMed: 15296736 
• DOI: https://doi.org/10.1016/j.str.2004.05.014
• Primary Citation Related Structures: 
  1T3Q


• PubMed Abstract: 
  

  The soil bacterium Pseudomonas putida 86 uses quinoline as a sole source of carbon and energy. Quinoline 2-oxidoreductase (Qor) catalyzes the first metabolic step converting quinoline to 2-oxo-1,2-dihydroquinoline. Qor is a member of the molybdenum hydroxylases. The molybdenum ion is coordinated by two ene-dithiolate sulfur atoms, two oxo-ligands, and a catalytically crucial sulfido-ligand, whose position in the active site was controversial. The 1.8 A resolution crystal structure of Qor indicates that the sulfido-ligand occupies the equatorial position at the molybdenum ion. The structural comparison of Qor with the allopurinol-inhibited xanthine dehydrogenase from Rhodobacter capsulatus allows direct insight into the mechanism of substrate recognition and the identification of putative catalytic residues. The active site protein variants QorE743V and QorE743D were analyzed to assess the catalytic role of E743.

---

Organizational Affiliation: 
• Abteilung für Strukturforschung, Max-Planck-Institut für Biochemie, 82152 Martinsried, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

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

Macromolecule Content 

• Total Structure Weight: 271.6 kDa 
• Atom Count: 21,323 
• Modeled Residue Count: 2,466 
• Deposited Residue Count: 2,488 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
quinoline 2-oxidoreductase small subunit	A, D	168	Pseudomonas putida	Mutation(s): 0  EC: 1.3.99.17
UniProt
Find proteins for P72223 (Pseudomonas putida) Explore P72223  Go to UniProtKB:  P72223

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
quinoline 2-oxidoreductase large subunit	B, E	788	Pseudomonas putida	Mutation(s): 0  EC: 1.3.99.17
UniProt
Find proteins for P72224 (Pseudomonas putida) Explore P72224  Go to UniProtKB:  P72224

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
quinoline 2-oxidoreductase medium subunit	C, F	288	Pseudomonas putida	Mutation(s): 0  EC: 1.3.99.17
UniProt
Find proteins for P72222 (Pseudomonas putida) Explore P72222  Go to UniProtKB:  P72222

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	FA [auth F], R [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
MCN	AA [auth E], N [auth B]	PTERIN CYTOSINE DINUCLEOTIDE C19 H22 N8 O13 P2 S2 RBWYFPNWTRZKKZ-LOIMWUFNSA-N
FES	G [auth A], H [auth A], U [auth D], V [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
SMO	BA [auth E], O [auth B]	DIOXOSULFIDOMOLYBDENUM(VI) ION Mo O2 S BSDYLDOYZVCHEU-UHFFFAOYSA-N
SO4	J [auth B], K [auth B], L [auth B], M [auth B], W [auth E], X [auth E], Y [auth E], Z [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	CA [auth E], DA [auth E], EA [auth E], GA [auth F], I [auth A], P [auth B], Q [auth B], S [auth C], T [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.207 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 278.32	α = 90
b = 72.1	β = 127.98
c = 202.65	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
XDS	data reduction
AMoRE	phasing
CNS	refinement
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-14 
Deposition Author(s): Bonin, I., Martins, B.M., Purvanov, V., Fetzner, S., Huber, R., Dobbek, H.

Revision History  

• Version 1.0: 2004-09-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Advisory, Refinement description
• Version 1.4: 2023-08-23
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description