6VCH

Crystal structure of Nitrosotalea devanaterra carotenoid cleavage dioxygenase in complex with 3-hydroxy-beta-apo-14'-carotenal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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

  • 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 ...

    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

    Research Service, Veterans Affairs Long Beach Healthcare System, Long Beach, CA 90822.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
carotenoid cleavage dioxygenaseABCDEF472Candidatus Nitrosotalea devanaterraMutation(s): 0 
Gene Names: NDEV_1113
Find proteins for A0A128A3G4 (Candidatus Nitrosotalea devanaterra)
Explore A0A128A3G4 
Go to UniProtKB:  A0A128A3G4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QVM
Query on QVM

Download CCD File 
A, B, C, D
(2E,4E,6E,8E,10E)-11-[(4R)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-5,9-dimethylundeca-2,4,6,8,10-pentaenal
C22 H30 O2
BCNPTKKIVMTZFO-UWYNECTCSA-N
 Ligand Interaction
CO
Query on CO

Download CCD File 
A, B, C, D, E, F
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.25α = 90
b = 107.25β = 90
c = 490.238γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

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 

  • 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