5F2C

Thermostable aldehyde dehydrogenase from Pyrobaculum sp. 1860 crystallized in microgravity (complex with NADP+)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

NADP-Dependent Aldehyde Dehydrogenase from ArchaeonPyrobaculum sp.1860: Structural and Functional Features.

Bezsudnova, E.Y.Petrova, T.E.Artemova, N.V.Boyko, K.M.Shabalin, I.G.Rakitina, T.V.Polyakov, K.M.Popov, V.O.

(2016) Archaea 2016: 9127857-9127857

  • DOI: https://doi.org/10.1155/2016/9127857
  • Primary Citation of Related Structures:  
    5EEB, 5EK6, 5EUY, 5EXF, 5F2C

  • PubMed Abstract: 

    We present the functional and structural characterization of the first archaeal thermostable NADP-dependent aldehyde dehydrogenase AlDHPyr1147. In vitro , AlDHPyr1147 catalyzes the irreversible oxidation of short aliphatic aldehydes at 60-85°С, and the affinity of AlDHPyr1147 to the NADP+ at 60°С is comparable to that for mesophilic analogues at 25°С. We determined the structures of the apo form of AlDHPyr1147 (3.04 Å resolution), three binary complexes with the coenzyme (1.90, 2.06, and 2.19 Å), and the ternary complex with the coenzyme and isobutyraldehyde as a substrate (2.66 Å). The nicotinamide moiety of the coenzyme is disordered in two binary complexes, while it is ordered in the ternary complex, as well as in the binary complex obtained after additional soaking with the substrate. AlDHPyr1147 structures demonstrate the strengthening of the dimeric contact (as compared with the analogues) and the concerted conformational flexibility of catalytic Cys287 and Glu253, as well as Leu254 and the nicotinamide moiety of the coenzyme. A comparison of the active sites of AlDHPyr1147 and dehydrogenases characterized earlier suggests that proton relay systems, which were previously proposed for dehydrogenases of this family, are blocked in AlDHPyr1147, and the proton release in the latter can occur through the substrate channel.


  • Organizational Affiliation

    A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, Bld. 2, Moscow 119071, Russia; Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H
491Pyrobaculum ferrireducensMutation(s): 0 
Gene Names: P186_1147
UniProt
Find proteins for G7VCG0 (Pyrobaculum ferrireducens)
Explore G7VCG0 
Go to UniProtKB:  G7VCG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7VCG0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
L [auth C]
M [auth D]
N [auth E]
I [auth A],
K [auth B],
L [auth C],
M [auth D],
N [auth E],
O [auth F],
P [auth G],
Q [auth H]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.356α = 90
b = 208.296β = 90
c = 163.811γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description