Crystal structure of Nitrosotalea devanaterra carotenoid cleavage dioxygenase, cobalt form

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 

Starting Model: experimental
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Structural basis for carotenoid cleavage by an archaeal carotenoid dioxygenase.

Daruwalla, A.Zhang, J.Lee, H.J.Khadka, N.Farquhar, E.R.Shi, W.von Lintig, J.Kiser, P.D.

(2020) Proc Natl Acad Sci U S A 117: 19914-19925

  • DOI: https://doi.org/10.1073/pnas.2004116117
  • Primary Citation of Related Structures:  
    6VCF, 6VCG, 6VCH

  • PubMed Abstract: 

    Apocarotenoids are important signaling molecules generated from carotenoids through the action of carotenoid cleavage dioxygenases (CCDs). These enzymes have a remarkable ability to cleave carotenoids at specific alkene bonds while leaving chemically similar sites within the polyene intact. Although several bacterial and eukaryotic CCDs have been characterized, the long-standing goal of experimentally visualizing a CCD-carotenoid complex at high resolution to explain this exquisite regioselectivity remains unfulfilled. CCD genes are also present in some archaeal genomes, but the encoded enzymes remain uninvestigated. Here, we address this knowledge gap through analysis of a metazoan-like archaeal CCD from Candidatus Nitrosotalea devanaterra ( Nd CCD). Nd CCD was active toward β-apocarotenoids but did not cleave bicyclic carotenoids. It exhibited an unusual regiospecificity, cleaving apocarotenoids solely at the C14'-C13' alkene bond to produce β-apo-14'-carotenals. The structure of Nd CCD revealed a tapered active site cavity markedly different from the broad active site observed for the retinal-forming Synechocystis apocarotenoid oxygenase ( Syn ACO) but similar to the vertebrate retinoid isomerase RPE65. The structure of Nd CCD in complex with its apocarotenoid product demonstrated that the site of cleavage is defined by interactions along the substrate binding cleft as well as selective stabilization of reaction intermediates at the scissile alkene. These data on the molecular basis of CCD catalysis shed light on the origins of the varied catalytic activities found in metazoan CCDs, opening the possibility of modifying their activity through rational chemical or genetic approaches.

  • Organizational Affiliation

    Department of Physiology & Biophysics, University of California School of Medicine, Irvine, CA 92617.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
carotenoid cleavage dioxygenase
A, B, C, D, E
A, B, C, D, E, F
472Candidatus Nitrosotalea devanaterraMutation(s): 0 
Gene Names: NDEV_1113
Find proteins for A0A128A3G4 (Candidatus Nitrosotalea devanaterra)
Explore A0A128A3G4 
Go to UniProtKB:  A0A128A3G4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A128A3G4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CO (Subject of Investigation/LOI)
Query on CO

Download Ideal Coordinates CCD File 
G [auth A]
H [auth B]
J [auth C]
M [auth D]
N [auth E]
G [auth A],
H [auth B],
J [auth C],
M [auth D],
N [auth E],
P [auth F]
Query on CL

Download Ideal Coordinates CCD File 
L [auth C],
O [auth E]
Query on NA

Download Ideal Coordinates CCD File 
I [auth B],
K [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.01α = 90
b = 108.01β = 90
c = 491.61γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesEY009339

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references, Derived calculations
  • Version 1.2: 2020-08-19
    Changes: Database references
  • Version 1.3: 2020-09-02
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description