6QAK

Structure of human ALDH9 in P21212 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Kinetic and structural analysis of human ALDH9A1.

Koncitikova, R.Vigouroux, A.Kopecna, M.Sebela, M.Morera, S.Kopecny, D.

(2019) Biosci Rep 39

  • DOI: 10.1042/BSR20190558
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Aldehyde dehydrogenases (ALDHs) constitute a superfamily of NAD(P) + -dependent enzymes, which detoxify aldehydes produced in various metabolic pathways to the corresponding carboxylic acids. Among the 19 human ALDHs, the cytosolic ALDH9A1 ...

    Aldehyde dehydrogenases (ALDHs) constitute a superfamily of NAD(P) + -dependent enzymes, which detoxify aldehydes produced in various metabolic pathways to the corresponding carboxylic acids. Among the 19 human ALDHs, the cytosolic ALDH9A1 has so far never been fully enzymatically characterized and its structure is still unknown. Here, we report complete molecular and kinetic properties of human ALDH9A1 as well as three crystal forms at 2.3, 2.9, and 2.5 Å resolution. We show that ALDH9A1 exhibits wide substrate specificity to aminoaldehydes, aliphatic and aromatic aldehydes with a clear preference for γ -trimethylaminobutyraldehyde (TMABAL). The structure of ALDH9A1 reveals that the enzyme assembles as a tetramer. Each ALDH monomer displays a typical ALDHs fold composed of an oligomerization domain, a coenzyme domain, a catalytic domain, and an inter-domain linker highly conserved in amino-acid sequence and folding. Nonetheless, structural comparison reveals a position and a fold of the inter-domain linker of ALDH9A1 never observed in any other ALDH so far. This unique difference is not compatible with the presence of a bound substrate and a large conformational rearrangement of the linker up to 30 Å has to occur to allow the access of the substrate channel. Moreover, the αβE region consisting of an α-helix and a β-strand of the coenzyme domain at the dimer interface are disordered, likely due to the loss of interactions with the inter-domain linker, which leads to incomplete β-nicotinamide adenine dinucleotide (NAD + ) binding pocket.


    Organizational Affiliation

    Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic david.kopecny@upol solange.morera@i2bc.paris-saclay.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-trimethylaminobutyraldehyde dehydrogenaseA, B, C, D, E, F, G, H508Homo sapiensMutation(s): 0 
Gene Names: ALDH9A1ALDH4ALDH7ALDH9
EC: 1.2.1.47 (PDB Primary Data), 1.2.1.3 (PDB Primary Data), 1.2.1.19 (PDB Primary Data)
Find proteins for P49189 (Homo sapiens)
Explore P49189 
Go to UniProtKB:  P49189
NIH Common Fund Data Resources
PHAROS  P49189
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.38α = 90
b = 159.59β = 90
c = 160.61γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references