Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 74.82 kDa 
• Atom Count: 6286 
• Modelled Residue Count: 670 
• Deposited Residue Count: 677 
• Unique protein chains: 1

1KB0

Crystal Structure of Quinohemoprotein Alcohol Dehydrogenase from Comamonas testosteroni

• PDB DOI: 10.2210/pdb1KB0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Comamonas testosteroni
• Mutation(s): Yes 


• Deposited: 2001-11-05 Released: 2001-12-28 
• Deposition Author(s): Rozeboom, H.J., Oubrie, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.188 
• R-Value Work: 0.160 
• R-Value Observed: 0.160 

Literature

Crystal structure of quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni: structural basis for substrate oxidation and electron transfer.

Oubrie, A., Rozeboom, H.J., Kalk, K.H., Huizinga, E.G., Dijkstra, B.W.

(2002) J Biol Chem 277: 3727-3732

• PubMed: 11714714 
• DOI: 10.1074/jbc.M109403200
• Primary Citation of Related Structures:  
  1KB0


• PubMed Abstract: 
  

Quinoprotein alcohol dehydrogenases are redox enzymes that participate in distinctive catabolic pathways that enable bacteria to grow on various alcohols as the sole source of carbon and energy. The x-ray structure of the quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni has been determined at 1.44 A resolution. It comprises two domains. The N-terminal domain has a beta-propeller fold and binds one pyrroloquinoline quinone cofactor and one calcium ion in the active site. A tetrahydrofuran-2-carboxylic acid molecule is present in the substrate-binding cleft. The position of this oxidation product provides valuable information on the amino acid residues involved in the reaction mechanism and their function. The C-terminal domain is an alpha-helical type I cytochrome c with His(608) and Met(647) as heme-iron ligands. This is the first reported structure of an electron transfer system between a quinoprotein alcohol dehydrogenase and cytochrome c. The shortest distance between pyrroloquinoline quinone and heme c is 12.9 A, one of the longest physiological edge-to-edge distances yet determined between two redox centers. A highly unusual disulfide bond between two adjacent cysteines bridges the redox centers. It appears essential for electron transfer. A water channel delineates a possible pathway for proton transfer from the active site to the solvent.

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Related Citations: 

• Crystallization of quinohaemoprotein alcohol dehydrogenase from Comamonas testosteroni: crystals with unique optical properties.
  Oubrie, A., Huizinga, E.G., Rozeboom, H.J., Kalk, K.H., de Jong, G.A., Duine, J.A., Dijkstra, B.W.
  (2001) Acta Crystallogr D Biol Crystallogr 57: 1732

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Organizational Affiliation: 

Laboratory of Biophysical Chemistry and BIOSON Research Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
quinohemoprotein alcohol dehydrogenase	A	677	Comamonas testosteroni	Mutation(s): 1  Gene Names: qheDH EC: 1.1.99 (PDB Primary Data), 1.1.9.1 (UniProt)
UniProt
Find proteins for Q46444 (Comamonas testosteroni) Explore Q46444  Go to UniProtKB:  Q46444

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	C [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
PQQ	E [auth A]	PYRROLOQUINOLINE QUINONE C14 H6 N2 O8 MMXZSJMASHPLLR-UHFFFAOYSA-N
TFB	D [auth A]	TETRAHYDROFURAN-2-CARBOXYLIC ACID C5 H8 O3 UJJLJRQIPMGXEZ-BYPYZUCNSA-N
GOL	F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TRO	A	L-PEPTIDE LINKING	C11 H12 N2 O3		TRP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.188 
• R-Value Work: 0.160 
• R-Value Observed: 0.160 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.92	α = 90
b = 74.331	β = 105.67
c = 92.332	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-05 
• Released Date: 2001-12-28 
Deposition Author(s): Rozeboom, H.J., Oubrie, A.

Revision History  

• Version 1.0: 2001-12-28
  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