1KV9 | pdb_00001kv9

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

PDB DOI: https://doi.org/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.189 (Depositor), 0.183 (DCC)
R-Value Work:
0.154 (Depositor), 0.149 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.2 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: 12057198 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(02)00774-8
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 74.09 kDa
Atom Count: 5,928
Modeled Residue Count: 664
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYPE II QUINOHEMOPROTEIN ALCOHOL DEHYDROGENASE	A	668	Pseudomonas putida	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8GR64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PQQ Query on PQQ Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PYRROLOQUINOLINE QUINONE C₁₄ H₆ N₂ O₈ MMXZSJMASHPLLR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ACN Query on ACN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ACETONE C₃ H₆ O CSCPPACGZOOCGX-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.189 (Depositor), 0.183 (DCC)
R-Value Work: 0.154 (Depositor), 0.149 (DCC)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2002-07-10

Deposition Author(s):

Revision History (Full details and data files)

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
Version 2.1: 2023-08-16
Changes: Data collection, Database references, Refinement description
Version 2.2: 2024-11-06
Changes: Structure summary