4A0M | pdb_00004a0m

CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE FROM SPINACH IN COMPLEX WITH NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Amino Acid Residues Critical for the Specificity for Betaine Aldehyde of the Plant Aldh10 Isoenzyme Involved in the Synthesis of Glycine Betaine.

Diaz-Sanchez, A.G.Gonzalez-Segura, L.Mujica-Jimenez, C.Rudino-Pinera, E.Montiel, C.Martinez-Castilla, L.P.Munoz-Clares, R.A.

(2012) Plant Physiol 158: 1570

  • DOI: https://doi.org/10.1104/pp.112.194514
  • Primary Citation Related Structures: 
    4A0M

  • PubMed Abstract: 

    Plant Aldehyde Dehydrogenase10 (ALDH10) enzymes catalyze the oxidation of ω-primary or ω-quaternary aminoaldehydes, but, intriguingly, only some of them, such as the spinach (Spinacia oleracea) betaine aldehyde dehydrogenase (SoBADH), efficiently oxidize betaine aldehyde (BAL) forming the osmoprotectant glycine betaine (GB), which confers tolerance to osmotic stress. The crystal structure of SoBADH reported here shows tyrosine (Tyr)-160, tryptophan (Trp)-167, Trp-285, and Trp-456 in an arrangement suitable for cation-π interactions with the trimethylammonium group of BAL. Mutation of these residues to alanine (Ala) resulted in significant K(m)(BAL) increases and V(max)/K(m)(BAL) decreases, particularly in the Y160A mutant. Tyr-160 and Trp-456, strictly conserved in plant ALDH10s, form a pocket where the bulky trimethylammonium group binds. This space is reduced in ALDH10s with low BADH activity, because an isoleucine (Ile) pushes the Trp against the Tyr. Those with high BADH activity instead have Ala (Ala-441 in SoBADH) or cysteine, which allow enough room for binding of BAL. Accordingly, the mutation A441I decreased the V(max)/K(m)(BAL) of SoBADH approximately 200 times, while the mutation A441C had no effect. The kinetics with other ω-aminoaldehydes were not affected in the A441I or A441C mutant, demonstrating that the existence of an Ile in the second sphere of interaction of the aldehyde is critical for discriminating against BAL in some plant ALDH10s. A survey of the known sequences indicates that plants have two ALDH10 isoenzymes: those known to be GB accumulators have a high-BAL-affinity isoenzyme with Ala or cysteine in this critical position, while non GB accumulators have low-BAL-affinity isoenzymes containing Ile. Therefore, BADH activity appears to restrict GB synthesis in non-GB-accumulator plants.


  • Organizational Affiliation
    • Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Mexico Distrito Federal, Mexico.

Macromolecule Content 

  • Total Structure Weight: 220.53 kDa 
  • Atom Count: 16,124 
  • Modeled Residue Count: 1,976 
  • Deposited Residue Count: 1,984 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
A, B, C, D
496Spinacia oleraceaMutation(s): 0 
EC: 1.2.1.8 (PDB Primary Data), 1.2.1 (UniProt), 1.2.1.19 (UniProt), 1.2.1.47 (UniProt)
UniProt
Find proteins for P17202 (Spinacia oleracea)
Explore P17202 
Go to UniProtKB:  P17202
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17202
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B],
N [auth C],
S [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
O [auth C]
T [auth D]
U [auth D]
G [auth A],
H [auth A],
O [auth C],
T [auth D],
U [auth D],
V [auth D],
W [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
E [auth A]
I [auth A]
J [auth B]
L [auth B]
M [auth C]
E [auth A],
I [auth A],
J [auth B],
L [auth B],
M [auth C],
P [auth C],
Q [auth C],
R [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.406α = 79.06
b = 80.979β = 84.94
c = 85.54γ = 77.99
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Other
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description