3VZ2

Structural insights into substrate and cofactor selection by sp2771


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

Starting Model: experimental
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This is version 1.1 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.R.

(2013) J Struct Biol 182: 125-135

  • DOI: https://doi.org/10.1016/j.jsb.2013.03.001
  • Primary Citation of Related Structures:  
    3VZ0, 3VZ1, 3VZ2, 3VZ3

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate-semialdehyde dehydrogenase
A, B
470Picosynechococcus sp. PCC 7002Mutation(s): 1 
Gene Names: SYNPCC7002_A2771
UniProt
Find proteins for B1XMM6 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6))
Explore B1XMM6 
Go to UniProtKB:  B1XMM6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1XMM6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.928α = 90
b = 116.963β = 90
c = 180.604γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description