6JZU

The crystal structure of acyl-acyl carrier protein (acyl-ACP) reductase (AAR) in complex with aldehyde deformylating oxygenase (ADO)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural insights into catalytic mechanism and product delivery of cyanobacterial acyl-acyl carrier protein reductase.

Gao, Y.Zhang, H.Fan, M.Jia, C.Shi, L.Pan, X.Cao, P.Zhao, X.Chang, W.Li, M.

(2020) Nat Commun 11: 1525-1525

  • DOI: https://doi.org/10.1038/s41467-020-15268-y
  • Primary Citation of Related Structures:  
    6JZQ, 6JZU, 6JZY, 6JZZ

  • PubMed Abstract: 

    Long-chain alk(a/e)nes represent the major constituents of conventional transportation fuels. Biosynthesis of alkanes is ubiquitous in many kinds of organisms. Cyanobacteria possess two enzymes, acyl-acyl carrier protein (acyl-ACP) reductase (AAR) and aldehyde-deformylating oxygenase (ADO), which function in a two-step alkane biosynthesis pathway. These two enzymes act in series and possibly form a complex that efficiently converts long chain fatty acyl-ACP/fatty acyl-CoA into hydrocarbon. While the structure of ADO has been previously described, structures of both AAR and AAR-ADO complex have not been solved, preventing deeper understanding of this pathway. Here, we report a ligand-free AAR structure, and three AAR-ADO complex structures in which AARs bind various ligands. Our results reveal the binding pattern of AAR with its substrate/cofactor, and suggest a potential aldehyde-transferring channel from AAR to ADO. Based on our structural and biochemical data, we proposed a model for the complete catalytic cycle of AAR.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Long-chain acyl-[acyl-carrier-protein] reductase341Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: Synpcc7942_1594SEC0028
EC: 1.2.1.80
UniProt
Find proteins for Q54765 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q54765 
Go to UniProtKB:  Q54765
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54765
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde decarbonylase254Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: SEC0027
EC: 4.1.99.5
UniProt
Find proteins for Q8KPT4 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805))
Explore Q8KPT4 
Go to UniProtKB:  Q8KPT4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KPT4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.377α = 90
b = 71.313β = 90
c = 137.137γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaKey Research Program of Frontier Sciences QYZDB-SSW-SMC005
Chinese Academy of SciencesChinaStrategic Priority Research Program XDB27020106
Chinese Academy of SciencesChinaStrategic Priority Research Program XDB08020302
National Natural Science Foundation of ChinaChina31770778
Ministry of Science and Technology (China)ChinaNational Key R&D Program of China 2017YFA0503702
Ministry of Science and Technology (China)ChinaNational Key R&D Program of China 2011CBA00900

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description