4RC7

Crystal structure of cyanobacterial aldehyde-deformylating oxygenase F86YF87Y mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural insights into the catalytic mechanism of aldehyde-deformylating oxygenases

Jia, C.Li, M.Li, J.Zhang, J.Zhang, H.Cao, P.Pan, X.Lu, X.Chang, W.

(2014) Protein Cell --: --

  • DOI: 10.1007/s13238-014-0108-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The fatty alk(a/e)ne biosynthesis pathway found in cyanobacteria gained tremendous attention in recent years as a promising alternative approach for biofuel production. Cyanobacterial aldehyde-deformylating oxygenase (cADO), which catalyzes the conve ...

    The fatty alk(a/e)ne biosynthesis pathway found in cyanobacteria gained tremendous attention in recent years as a promising alternative approach for biofuel production. Cyanobacterial aldehyde-deformylating oxygenase (cADO), which catalyzes the conversion of Cn fatty aldehyde to its corresponding Cn-1 alk(a/e)ne, is a key enzyme in that pathway. Due to its low activity, alk(a/e)ne production by cADO is an inefficient process. Previous biochemical and structural investigations of cADO have provided some information on its catalytic reaction. However, the details of its catalytic processes remain unclear. Here we report five crystal structures of cADO from the Synechococcus elongates strain PCC7942 in both its iron-free and iron-bound forms, representing different states during its catalytic process. Structural comparisons and functional enzyme assays indicate that Glu144, one of the iron-coordinating residues, plays a vital role in the catalytic reaction of cADO. Moreover, the helix where Glu144 resides exhibits two distinct conformations that correlates with the different binding states of the di-iron center in cADO structures. Therefore, our results provide a structural explanation for the highly labile feature of cADO di-iron center, which we proposed to be related to its low enzymatic activity. On the basis of our structural and biochemical data, a possible catalytic process of cADO was proposed, which could aid the design of cADO with improved activity.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aldehyde decarbonylase
A
220Synechococcus elongatus (strain PCC 7942)Mutation(s): 2 
EC: 4.1.99.5
Find proteins for Q54764 (Synechococcus elongatus (strain PCC 7942))
Go to UniProtKB:  Q54764
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Aldehyde decarbonylase
B
222Synechococcus elongatus (strain PCC 7942)Mutation(s): 2 
EC: 4.1.99.5
Find proteins for Q54764 (Synechococcus elongatus (strain PCC 7942))
Go to UniProtKB:  Q54764
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PL3
Query on PL3

Download SDF File 
Download CCD File 
A, B
HEXADECAN-1-OL
C16 H34 O
BXWNKGSJHAJOGX-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.014α = 90.00
b = 62.109β = 90.00
c = 125.003γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
ADSCdata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release