8FTY

Crystal structure of the carotenoid isomerooxygenase, NinaB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Carotenoid cleavage enzymes evolved convergently to generate the visual chromophore.

Solano, Y.J.Everett, M.P.Dang, K.S.Abueg, J.Kiser, P.D.

(2024) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-024-01554-z
  • Primary Citation of Related Structures:  
    8FTY

  • PubMed Abstract: 

    The retinal light response in animals originates from the photoisomerization of an opsin-coupled 11-cis-retinaldehyde chromophore. This visual chromophore is enzymatically produced through the action of carotenoid cleavage dioxygenases. Vertebrates require two carotenoid cleavage dioxygenases, β-carotene oxygenase 1 and retinal pigment epithelium 65 (RPE65), to form 11-cis-retinaldehyde from carotenoid substrates, whereas invertebrates such as insects use a single enzyme known as Neither Inactivation Nor Afterpotential B (NinaB). RPE65 and NinaB couple trans-cis isomerization with hydrolysis and oxygenation, respectively, but the mechanistic relationship of their isomerase activities remains unknown. Here we report the structure of NinaB, revealing details of its active site architecture and mode of membrane binding. Structure-guided mutagenesis studies identify a residue cluster deep within the NinaB substrate-binding cleft that controls its isomerization activity. Our data demonstrate that isomerization activity is mediated by distinct active site regions in NinaB and RPE65-an evolutionary convergence that deepens our understanding of visual system diversity.


  • Organizational Affiliation

    Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
carotenoid isomerooxygenase
A, B, C, D
509Trichoplusia niMutation(s): 0 
Gene Names: LOC113497779
UniProt
Find proteins for A0A7E5VY83 (Trichoplusia ni)
Explore A0A7E5VY83 
Go to UniProtKB:  A0A7E5VY83
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7E5VY83
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
carotenoid isomerooxygenase
E, F
509Trichoplusia niMutation(s): 0 
Gene Names: LOC113497779
UniProt
Find proteins for A0A7E5VY83 (Trichoplusia ni)
Explore A0A7E5VY83 
Go to UniProtKB:  A0A7E5VY83
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7E5VY83
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
carotenoid isomerooxygenase
G, H
509Trichoplusia niMutation(s): 0 
Gene Names: LOC113497779
UniProt
Find proteins for A0A7E5VY83 (Trichoplusia ni)
Explore A0A7E5VY83 
Go to UniProtKB:  A0A7E5VY83
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7E5VY83
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC

Download Ideal Coordinates CCD File 
EA [auth F]CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
MPD (Subject of Investigation/LOI)
Query on MPD

Download Ideal Coordinates CCD File 
CA [auth F]
DA [auth F]
GA [auth G]
HA [auth G]
J [auth A]
CA [auth F],
DA [auth F],
GA [auth G],
HA [auth G],
J [auth A],
JA [auth H],
L [auth A],
N [auth B],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
X [auth E],
Y [auth E],
Z [auth E]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
BA [auth F]
FA [auth G]
I [auth A]
IA [auth H]
M [auth B]
BA [auth F],
FA [auth G],
I [auth A],
IA [auth H],
M [auth B],
O [auth C],
R [auth D],
W [auth E]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth E],
K [auth A],
U [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
V [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
E, F
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
CSD
Query on CSD
G, H
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 349.934α = 90
b = 52.036β = 98.95
c = 210.036γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-2107713

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Derived calculations
  • Version 1.2: 2024-02-21
    Changes: Database references