5U0L

X-ray crystal structure of fatty aldehyde dehydrogenase enzymes from Marinobacter aquaeolei VT8 complexed with a substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.285 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Five Fatty Aldehyde Dehydrogenase Enzymes from Marinobacter and Acinetobacter spp. and Structural Insights into the Aldehyde Binding Pocket.

Bertram, J.H.Mulliner, K.M.Shi, K.Plunkett, M.H.Nixon, P.Serratore, N.A.Douglas, C.J.Aihara, H.Barney, B.M.

(2017) Appl. Environ. Microbiol. 83: --

  • DOI: 10.1128/AEM.00018-17
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enzymes involved in lipid biosynthesis and metabolism play an important role in energy conversion and storage and in the function of structural components such as cell membranes. The fatty aldehyde dehydrogenase (FAldDH) plays a central function in t ...

    Enzymes involved in lipid biosynthesis and metabolism play an important role in energy conversion and storage and in the function of structural components such as cell membranes. The fatty aldehyde dehydrogenase (FAldDH) plays a central function in the metabolism of lipid intermediates, oxidizing fatty aldehydes to the corresponding fatty acid and competing with pathways that would further reduce the fatty aldehydes to fatty alcohols or require the fatty aldehydes to produce alkanes. In this report, the genes for four putative FAldDH enzymes from Marinobacter aquaeolei VT8 and an additional enzyme from Acinetobacter baylyi were heterologously expressed in Escherichia coli and shown to display FAldDH activity. Five enzymes (Maqu_0438, Maqu_3316, Maqu_3410, Maqu_3572, and the enzyme reported under RefSeq accession no. WP_004927398) were found to act on aldehydes ranging from acetaldehyde to hexadecanal and also acted on the unsaturated long-chain palmitoleyl and oleyl aldehydes. A comparison of the specificities of these enzymes with various aldehydes is presented. Crystallization trials yielded diffraction-quality crystals of one particular FAldDH (Maqu_3316) from M. aquaeolei VT8. Crystals were independently treated with both the NAD+ cofactor and the aldehyde substrate decanal, revealing specific details of the likely substrate binding pocket for this class of enzymes. A likely model for how catalysis by the enzyme is accomplished is also provided.IMPORTANCE This study provides a comparison of multiple enzymes with the ability to oxidize fatty aldehydes to fatty acids and provides a likely picture of how the fatty aldehyde and NAD+ are bound to the enzyme to facilitate catalysis. Based on the information obtained from this structural analysis and comparisons of specificities for the five enzymes that were characterized, correlations to the potential roles played by specific residues within the structure may be drawn.


    Organizational Affiliation

    Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, Minnesota, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-succinylglutamate 5-semialdehyde dehydrogenase
A, B
497Marinobacter hydrocarbonoclasticus (strain ATCC 700491 / DSM 11845 / VT8)Mutation(s): 0 
Gene Names: astD
EC: 1.2.1.71
Find proteins for A1U5W8 (Marinobacter hydrocarbonoclasticus (strain ATCC 700491 / DSM 11845 / VT8))
Go to UniProtKB:  A1U5W8
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

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B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
8YP
Query on 8YP

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A
decanal
C10 H20 O
KSMVZQYAVGTKIV-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.285 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.214 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.710α = 90.00
b = 98.710β = 90.00
c = 254.725γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118047
National Science Foundation (NSF, United States)United StatesCBET-1437758
National Science Foundation (NSF, United States)United States0968781

Revision History 

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-06-14
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence
  • Version 1.3: 2019-11-27
    Type: Author supporting evidence