3EFV

Crystal Structure of a Putative Succinate-Semialdehyde Dehydrogenase from Salmonella typhimurium LT2 with bound NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure and activity of the NAD(P)(+) -dependent succinate semialdehyde dehydrogenase YneI from Salmonella typhimurium.

Zheng, H.Beliavsky, A.Tchigvintsev, A.Brunzelle, J.S.Brown, G.Flick, R.Evdokimova, E.Wawrzak, Z.Mahadevan, R.Anderson, W.F.Savchenko, A.Yakunin, A.F.

(2013) Proteins 81: 1031-1041

  • DOI: 10.1002/prot.24227
  • Primary Citation of Related Structures:  3ETF

  • PubMed Abstract: 
  • Aldehyde dehydrogenases are found in all organisms and play an important role in the metabolic conversion and detoxification of endogenous and exogenous aldehydes. Genomes of many organisms including Escherichia coli and Salmonella typhimurium encode ...

    Aldehyde dehydrogenases are found in all organisms and play an important role in the metabolic conversion and detoxification of endogenous and exogenous aldehydes. Genomes of many organisms including Escherichia coli and Salmonella typhimurium encode two succinate semialdehyde dehydrogenases with low sequence similarity and different cofactor preference (YneI and GabD). Here, we present the crystal structure and biochemical characterization of the NAD(P)(+)-dependent succinate semialdehyde dehydrogenase YneI from S. typhimurium. This enzyme shows high activity and affinity toward succinate semialdehyde and exhibits substrate inhibition at concentrations of SSA higher than 0.1 mM. YneI can use both NAD(+) and NADP(+) as cofactors, although affinity to NAD(+) is 10 times higher. High resolution crystal structures of YneI were solved in a free state (1.85 Å) and in complex with NAD(+) (1.90 Å) revealing a two domain protein with the active site located in the interdomain interface. The NAD(+) molecule is bound in the long channel with its nicotinamide ring positioned close to the side chain of the catalytic Cys268. Site-directed mutagenesis demonstrated that this residue, as well as the conserved Trp136, Glu365, and Asp426 are important for activity of YneI, and that the conserved Lys160 contributes to the enzyme preference to NAD(+) . Our work has provided further insight into the molecular mechanisms of substrate selectivity and activity of succinate semialdehyde dehydrogenases.


    Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative succinate-semialdehyde dehydrogenase
A, B, C, D
462Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Gene Names: yneI
EC: 1.2.1.-
Find proteins for Q8ZPI3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  Q8ZPI3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 133.826α = 90.00
b = 133.826β = 90.00
c = 245.276γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SHELXDphasing
HKL-2000data scaling
HKL-2000data reduction
BLU-MAXdata collection
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-12-14
    Type: Structure summary
  • Version 1.3: 2012-12-19
    Type: Database references
  • Version 1.4: 2013-06-12
    Type: Database references