3VZ0

Structural insights into cofactor and substrate selection by Gox0499


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for cofactor and substrate selection by cyanobacterium succinic semialdehyde dehydrogenase

Yuan, Z.Yin, B.Wei, D.Yuan, Y.A.

(2013) J.Struct.Biol. 182: 125-135

  • DOI: 10.1016/j.jsb.2013.03.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aldehyde dehydrogenase (ALDH) catalyzes the oxidation of aldehydes to carboxylic acids. Cyanobacterium Synechococcus contains one ALDH enzyme (Sp2771), together with a novel 2-oxoglutarate decarboxylase, to complete a non-canonical tricarboxylic acid ...

    Aldehyde dehydrogenase (ALDH) catalyzes the oxidation of aldehydes to carboxylic acids. Cyanobacterium Synechococcus contains one ALDH enzyme (Sp2771), together with a novel 2-oxoglutarate decarboxylase, to complete a non-canonical tricarboxylic acid cycle. However, the molecular mechanisms for substrate selection and cofactor preference by Sp2771 are largely unknown. Here, we report crystal structures of wild type Sp2771, Sp2771 S419A mutant and ternary structure of Sp2771 C262A mutant in complex with NADP(+) and SSA, as well as binary structure of Gluconobacter oxydans aldehyde dehydrogenase (Gox0499) in complex with PEG. Structural comparison of Sp2771 with Gox0499, coupled with mutational analysis, demonstrates that Ser157 residue in Sp2771 and corresponding Pro159 residue in Gox0499 play critical structural roles in determining NADP(+) and NAD(+) preference for Sp2771 and Gox0499, respectively, whereas size and distribution of hydrophobic residues along the substrate binding funnel determine substrate selection. Hence, our work has provided insightful structural information into cofactor and substrate selection by ALDH.


    Organizational Affiliation

    Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative NAD-dependent aldehyde dehydrogenase
A, B, C, D
459Gluconobacter oxydans (strain 621H)Mutation(s): 0 
Find proteins for Q5FTL8 (Gluconobacter oxydans (strain 621H))
Go to UniProtKB:  Q5FTL8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2PE
Query on 2PE

Download SDF File 
Download CCD File 
A, B, C, D
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.523α = 90.00
b = 254.602β = 90.00
c = 76.778γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
SHARPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release