6JZZ

The crystal structure of AAR-C294S in complex with ADO.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.213 

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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: 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 ...

    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. meili@ibp.ac.cn.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Long-chain acyl-[acyl-carrier-protein] reductaseA341Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 1 
Gene Names: Synpcc7942_1594, SEC0028
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
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Aldehyde decarbonylaseB254Synechococcus 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ST9 (Subject of Investigation/LOI)
Query on ST9
Download Ideal Coordinates CCD File 
C [auth A]STEAROYL-COENZYME A
C39 H70 N7 O17 P3 S
SIARJEKBADXQJG-LFZQUHGESA-N		 Ligand Interaction
PL3 (Subject of Investigation/LOI)
Query on PL3
Download Ideal Coordinates CCD File 
E [auth B]HEXADECAN-1-OL
C16 H34 O
BXWNKGSJHAJOGX-UHFFFAOYSA-N		 Ligand Interaction
FE2 (Subject of Investigation/LOI)
Query on FE2
Download Ideal Coordinates CCD File 
D [auth B],
F [auth B]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.527α = 90
b = 72.335β = 90
c = 137.196γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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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