8QMT

Succinic semialdehyde dehydrogenase from E. coli with Q262R substitution and bound NAD+, succinic semialdehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies.

He, H.Gomez-Coronado, P.A.Zarzycki, J.Barthel, S.Kahnt, J.Claus, P.Klein, M.Klose, M.de Crecy-Lagard, V.Schindler, D.Paczia, N.Glatter, T.Erb, T.J.

(2024) Nat Commun 15: 8898-8898

  • DOI: https://doi.org/10.1038/s41467-024-53156-x
  • Primary Citation of Related Structures:  
    8QMQ, 8QMR, 8QMS, 8QMT

  • PubMed Abstract: 

    Promiscuous enzymes often serve as the starting point for the evolution of novel functions. Yet, the extent to which the promiscuity of an individual enzyme can be harnessed several times independently for different purposes during evolution is poorly reported. Here, we present a case study illustrating how NAD(P) + -dependent succinate semialdehyde dehydrogenase of Escherichia coli (Sad) is independently recruited through various evolutionary mechanisms for distinct metabolic demands, in particular vitamin biosynthesis and central carbon metabolism. Using adaptive laboratory evolution (ALE), we show that Sad can substitute for the roles of erythrose 4-phosphate dehydrogenase in pyridoxal 5'-phosphate (PLP) biosynthesis and glyceraldehyde 3-phosphate dehydrogenase in glycolysis. To recruit Sad for PLP biosynthesis and glycolysis, ALE employs various mechanisms, including active site mutation, copy number amplification, and (de)regulation of gene expression. Our study traces down these different evolutionary trajectories, reports on the surprising active site plasticity of Sad, identifies regulatory links in amino acid metabolism, and highlights the potential of an ordinary enzyme as innovation reservoir for evolution.


  • Organizational Affiliation

    Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. hai.he@mpi-marburg.mpg.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate semialdehyde dehydrogenase [NAD(P)+] Sad
A, B, C, D
462Escherichia coli K-12Mutation(s): 1 
Gene Names: sadyneIb1525JW5247
EC: 1.2.1.16
UniProt
Find proteins for P76149 (Escherichia coli (strain K12))
Explore P76149 
Go to UniProtKB:  P76149
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76149
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SSN (Subject of Investigation/LOI)
Query on SSN

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
4-oxobutanoic acid
C4 H6 O3
UIUJIQZEACWQSV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.71α = 90
b = 115.11β = 90
c = 179.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Structure summary
  • Version 1.2: 2024-10-30
    Changes: Database references