1T3Q

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
R-Value Work: 0.186
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2004.05.014
Primary Citation of 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.

Macromolecule Content

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

Macromolecules

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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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P72223
Sequence Annotations Expand
Reference Sequence

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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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P72224
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P72222
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain FA [auth F] SDF format, chain R [auth C] MOL2 format, chain FA [auth F] MOL2 format, chain R [auth C]	FA [auth F], R [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain FA [auth F] Focus chain R [auth C] Interactions & Density Focus chain FA [auth F] Focus chain R [auth C]
MCN Query on MCN Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain N [auth B] MOL2 format, chain AA [auth E] MOL2 format, chain N [auth B]	AA [auth E], N [auth B]	PTERIN CYTOSINE DINUCLEOTIDE C₁₉ H₂₂ N₈ O₁₃ P₂ S₂ RBWYFPNWTRZKKZ-LOIMWUFNSA-N		Interactions Focus chain AA [auth E] Focus chain N [auth B] Interactions & Density Focus chain AA [auth E] Focus chain N [auth B]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain U [auth D]	G [auth A], H [auth A], U [auth D], V [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain U [auth D] Focus chain V [auth D]
SMO Query on SMO Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain O [auth B] MOL2 format, chain BA [auth E] MOL2 format, chain O [auth B]	BA [auth E], O [auth B]	DIOXOSULFIDOMOLYBDENUM(VI) ION Mo O₂ S BSDYLDOYZVCHEU-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain O [auth B] Interactions & Density Focus chain BA [auth E] Focus chain O [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain Z [auth E] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Y [auth E] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Y [auth E]	J [auth B] K [auth B] L [auth B] M [auth B] W [auth E] 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		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain GA [auth F] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C]	CA [auth E] DA [auth E] EA [auth E] GA [auth F] I [auth A] 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		Interactions Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.207
R-Value Work: 0.186
R-Value Observed: 0.186
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-09-14

Deposition Author(s):

Revision History (Full details and data files)

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

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Help and Resources

1T3Q

Crystal structure of quinoline 2-Oxidoreductase from Pseudomonas Putida 86

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)