1T3Q

Crystal structure of quinoline 2-Oxidoreductase from Pseudomonas Putida 86


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


This is version 1.3 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

  • DOI: 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 h ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
quinoline 2-oxidoreductase small subunitA, D168Pseudomonas putidaMutation(s): 0 
Gene Names: qorS
EC: 1.3.99.17
Find proteins for P72223 (Pseudomonas putida)
Explore P72223 
Go to UniProtKB:  P72223
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
quinoline 2-oxidoreductase large subunitB, E788Pseudomonas putidaMutation(s): 0 
Gene Names: qorL
EC: 1.3.99.17
Find proteins for P72224 (Pseudomonas putida)
Explore P72224 
Go to UniProtKB:  P72224
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
quinoline 2-oxidoreductase medium subunitC, F288Pseudomonas putidaMutation(s): 0 
Gene Names: qorMKF715C_ch5940
EC: 1.3.99.17
Find proteins for P72222 (Pseudomonas putida)
Explore P72222 
Go to UniProtKB:  P72222
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
C, F
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MCN
Query on MCN

Download CCD File 
B, E
PTERIN CYTOSINE DINUCLEOTIDE
C19 H22 N8 O13 P2 S2
RBWYFPNWTRZKKZ-LOIMWUFNSA-N
 Ligand Interaction
FES
Query on FES

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A, D
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
SMO
Query on SMO

Download CCD File 
B, E
DIOXOSULFIDOMOLYBDENUM(VI) ION
Mo O2 S
BSDYLDOYZVCHEU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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B, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B, C, E, F
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
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 = 278.32α = 90
b = 72.1β = 127.98
c = 202.65γ = 90
Software Package:
Software NamePurpose
MAR345data collection
XDSdata reduction
AMoREphasing
CNSrefinement
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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