1KV9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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 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 ...

    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.


    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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYPE II QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE
A
668Pseudomonas putidaGene Names: qbdA
EC: 1.1.9.1
Find proteins for Q8GR64 (Pseudomonas putida)
Go to UniProtKB:  Q8GR64
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
ACN
Query on ACN

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Download CCD File 
A
ACETONE
C3 H6 O
CSCPPACGZOOCGX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
PQQ
Query on PQQ

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Download CCD File 
A
PYRROLOQUINOLINE QUINONE
C14 H6 N2 O8
MMXZSJMASHPLLR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.154 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 54.807α = 89.65
b = 57.437β = 69.34
c = 67.523γ = 68.39
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SHARPphasing
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-07-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance