Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74.09 kDa 
• Atom Count: 5928 
• Modelled Residue Count: 664 
• Deposited Residue Count: 668 
• Unique protein chains: 1

1KV9

Structure at 1.9 A Resolution of a Quinohemoprotein Alcohol Dehydrogenase from Pseudomonas putida HK5

• PDB DOI: 10.2210/pdb1KV9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2002-01-25 Released: 2002-07-10 
• Deposition Author(s): Chen, Z.-W., Matsushita, K., Yamashita, T., Fujii, T., Toyama, H., Adachi, O., Bellamy, H.D., Mathews, F.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.189 
• R-Value Work: 0.154 

Literature

Structure at 1.9 A resolution of a quinohemoprotein alcohol dehydrogenase from Pseudomonas putida HK5.

Chen, Z.W., Matsushita, K., Yamashita, T., Fujii, T.A., Toyama, H., Adachi, O., Bellamy, H.D., Mathews, F.S.

(2002) Structure 10: 837-849

• PubMed: 12057198 
• DOI: 10.1016/s0969-2126(02)00774-8
• Primary Citation of Related Structures:  
  1KV9


• PubMed Abstract: 
  

The type II quinohemoprotein alcohol dehydrogenase of Pseudomonas putida is a periplasmic enzyme that oxidizes substrate alcohols to the aldehyde and transfers electrons first to pyrroloquinoline quinone (PQQ) and then to an internal heme group. The 1.9 A resolution crystal structure reveals that the enzyme contains a large N-terminal eight-stranded beta propeller domain (approximately 60 kDa) similar to methanol dehydrogenase and a small C-terminal c-type cytochrome domain (approximately 10 kDa) similar to the cytochrome subunit of p-cresol methylhydoxylase. The PQQ is bound near the axis of the propeller domain about 14 A from the heme. A molecule of acetone, the product of the oxidation of isopropanol present during crystallization, appears to be bound in the active site cavity.

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Related Citations: 

• Determination of the Gene Sequence and the Three-dimensional Structure at 2.4 Angstroms Resolution of Methanol Dehydrogenase from Methylophilus W3A1
  Xia, Z., Dai, W., Zhang, Y., White, S.A., Boyd, G.D., Mathews, F.S.
  (1996) J Mol Biol 259: 480

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYPE II QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE	A	668	Pseudomonas putida	Mutation(s): 0  Gene Names: qbdA EC: 1.1.99 (PDB Primary Data), 1.1.9.1 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q8GR64 (Pseudomonas putida) Explore Q8GR64  Go to UniProtKB:  Q8GR64

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	D [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
PQQ	C [auth A]	PYRROLOQUINOLINE QUINONE C14 H6 N2 O8 MMXZSJMASHPLLR-UHFFFAOYSA-N
EPE	E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACN	F [auth A]	ACETONE C3 H6 O CSCPPACGZOOCGX-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.189 
• R-Value Work: 0.154 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.807	α = 89.65
b = 57.437	β = 69.34
c = 67.523	γ = 68.39

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-01-25 
• Released Date: 2002-07-10 
Deposition Author(s): Chen, Z.-W., Matsushita, K., Yamashita, T., Fujii, T., Toyama, H., Adachi, O., Bellamy, H.D., Mathews, F.S.

Revision History  

• Version 1.0: 2002-07-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2021-03-03
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary