1KV9

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 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

  • 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 ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TYPE II QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASEA668Pseudomonas putidaMutation(s): 0 
Gene Names: qbdA
EC: 1.1.99 (PDB Primary Data), 1.1.9.1 (UniProt)
Find proteins for Q8GR64 (Pseudomonas putida)
Explore Q8GR64 
Go to UniProtKB:  Q8GR64
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
PQQ
Query on PQQ
Download CCD File 
A
PYRROLOQUINOLINE QUINONE
C14 H6 N2 O8
MMXZSJMASHPLLR-UHFFFAOYSA-N		 Ligand Interaction
EPE
Query on EPE
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ACN
Query on ACN
Download CCD File 
A
ACETONE
C3 H6 O
CSCPPACGZOOCGX-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
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 = 54.807α = 89.65
b = 57.437β = 69.34
c = 67.523γ = 68.39
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

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