1LLU | pdb_00001llu

THE TERNARY COMPLEX OF PSEUDOMONAS AERUGINOSA ALCOHOL DEHYDROGENASE WITH ITS COENZYME AND WEAK SUBSTRATE

PDB DOI: https://doi.org/10.2210/pdb1LLU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2002-04-30 Released: 2003-11-11
Deposition Author(s): Levin, I., Meiri, G., Peretz, M., Frolow, F., Burstein, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.246 (Depositor), 0.249 (DCC)
R-Value Work:
0.229 (Depositor), 0.234 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The ternary complex of Pseudomonas aeruginosa alcohol dehydrogenase with NADH and ethylene glycol.

Levin, I., Meiri, G., Peretz, M., Burstein, Y., Frolow, F.

(2004) Protein Sci 13: 1547-1556

PubMed: 15152088 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1110/ps.03531404
Primary Citation Related Structures:
1LLU

PubMed Abstract:
Pseudomonas aeruginosa alcohol dehydrogenase (PaADH; ADH, EC 1.1.1.1) catalyzes the reversible oxidation of primary and secondary alcohols to the corresponding aldehydes and ketones, using NAD as coenzyme. We crystallized the ternary complex of PaADH with its coenzyme and a substrate molecule and determined its structure at a resolution of 2.3 A, using the molecular replacement method. The PaADH tetramer comprises four identical chains of 342 amino acid residues each and obeys ~222-point symmetry. The PaADH monomer is structurally similar to alcohol dehydrogenase monomers from vertebrates, archaea, and bacteria. The stabilization of the ternary complex of PaADH, the coenzyme, and the poor substrate ethylene glycol (k(cat) = 4.5 sec(-1); Km > 200 mM) was due to the blocked exit of the coenzyme in the crystalline state, combined with a high (2.5 M) concentration of the substrate. The structure of the ternary complex presents the precise geometry of the Zn coordination complex, the proton-shuttling system, and the hydride transfer path. The ternary complex structure also suggests that the low efficiency of ethylene glycol as a substrate results from the presence of a second hydroxyl group in this molecule.

Organizational Affiliation

Department of Organic Chemistry, Weizmann Institute of Science, 76100 Rehovot, Israel.

Macromolecule Content

Total Structure Weight: 294.45 kDa
Atom Count: 21,580
Modeled Residue Count: 2,728
Deposited Residue Count: 2,736
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol Dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	342	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: adh EC: 1.1.1.1
UniProt
Find proteins for Q9HTD9 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HTD9 Go to UniProtKB: Q9HTD9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HTD9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain HA [auth F] SDF format, chain K [auth A] SDF format, chain LA [auth G] SDF format, chain P [auth B] SDF format, chain QA [auth H] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth H] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	CA [auth E] HA [auth F] K [auth A] LA [auth G] P [auth B] CA [auth E], HA [auth F], K [auth A], LA [auth G], P [auth B], QA [auth H], T [auth C], Y [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain CA [auth E] Focus chain HA [auth F] Focus chain K [auth A] Focus chain LA [auth G] Focus chain P [auth B] Focus chain QA [auth H] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain HA [auth F] Focus chain K [auth A] Focus chain LA [auth G] Focus chain P [auth B] Focus chain QA [auth H] Focus chain T [auth C] Focus chain Y [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain OA [auth H] SDF format, chain PA [auth H] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth H] MOL2 format, chain PA [auth H] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth H] mmCIF format, chain PA [auth H] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	AA [auth E] BA [auth E] FA [auth F] GA [auth F] I [auth A] AA [auth E], BA [auth E], FA [auth F], GA [auth F], I [auth A], J [auth A], JA [auth G], KA [auth G], N [auth B], O [auth B], OA [auth H], PA [auth H], R [auth C], S [auth C], W [auth D], X [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain N [auth B] Focus chain O [auth B] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain N [auth B] Focus chain O [auth B] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain IA [auth F] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth G] SDF format, chain NA [auth G] SDF format, chain Q [auth B] SDF format, chain RA [auth H] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain Z [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth H] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain NA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain RA [auth H] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D]	DA [auth E] EA [auth E] IA [auth F] L [auth A] M [auth A] DA [auth E], EA [auth E], IA [auth F], L [auth A], M [auth A], MA [auth G], NA [auth G], Q [auth B], RA [auth H], U [auth C], V [auth C], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain EA [auth E] Focus chain IA [auth F] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain Q [auth B] Focus chain RA [auth H] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain DA [auth E] Focus chain EA [auth E] Focus chain IA [auth F] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain Q [auth B] Focus chain RA [auth H] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.246 (Depositor), 0.249 (DCC)
R-Value Work: 0.229 (Depositor), 0.234 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.171	α = 79.34
b = 86.328	β = 78.66
c = 125.698	γ = 71.58

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-11-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-11-11
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-16
Changes: Data collection, Database references, Derived calculations, Refinement description