5U97

Crystal structure of Co-CAO1 in complex with piceatannol

  • Classification: OXIDOREDUCTASE
  • Organism(s): Neurospora crassa OR74A
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2016-12-15 Released: 2017-05-31 
  • Deposition Author(s): Sui, X., Palczewski, K., Banerjee, S., Kiser, P.D.
  • Funding Organization(s): National Institutes of Health/National Eye Institute (NIH/NEI), Burroughs Wellcome Fund, National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Veterans Affairs (VA, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structure and Spectroscopy of Alkene-Cleaving Dioxygenases Containing an Atypically Coordinated Non-Heme Iron Center.

Sui, X.Weitz, A.C.Farquhar, E.R.Badiee, M.Banerjee, S.von Lintig, J.Tochtrop, G.P.Palczewski, K.Hendrich, M.P.Kiser, P.D.

(2017) Biochemistry 56: 2836-2852

  • DOI: https://doi.org/10.1021/acs.biochem.7b00251
  • Primary Citation of Related Structures:  
    5U8X, 5U8Y, 5U8Z, 5U90, 5U97

  • PubMed Abstract: 

    Carotenoid cleavage oxygenases (CCOs) are non-heme iron enzymes that catalyze scission of alkene groups in carotenoids and stilbenoids to form biologically important products. CCOs possess a rare four-His iron center whose resting-state structure and interaction with substrates are incompletely understood. Here, we address this knowledge gap through a comprehensive structural and spectroscopic study of three phyletically diverse CCOs. The crystal structure of a fungal stilbenoid-cleaving CCO, CAO1, reveals strong similarity between its iron center and those of carotenoid-cleaving CCOs, but with a markedly different substrate-binding cleft. These enzymes all possess a five-coordinate high-spin Fe(II) center with resting-state Fe-His bond lengths of ∼2.15 Å. This ligand set generates an iron environment more electropositive than those of other non-heme iron dioxygenases as observed by Mössbauer isomer shifts. Dioxygen (O 2 ) does not coordinate iron in the absence of substrate. Substrates bind away (∼4.7 Å) from the iron and have little impact on its electronic structure, thus excluding coordination-triggered O 2 binding. However, substrate binding does perturb the spectral properties of CCO Fe-NO derivatives, indicating proximate organic substrate and O 2 -binding sites, which might influence Fe-O 2 interactions. Together, these data provide a robust description of the CCO iron center and its interactions with substrates and substrate mimetics that illuminates commonalities as well as subtle and profound structural differences within the CCO family.


  • Organizational Affiliation

    Department of Pharmacology, School of Medicine, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carotenoid oxygenase 1
A, B, C, D
526Neurospora crassa OR74AMutation(s): 0 
Gene Names: cao-1NCU07008
EC: 1.13.11
UniProt
Find proteins for Q7S860 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
Explore Q7S860 
Go to UniProtKB:  Q7S860
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7S860
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PIT (Subject of Investigation/LOI)
Query on PIT

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
K [auth B]
M [auth B]
F [auth A],
G [auth A],
H [auth A],
K [auth B],
M [auth B],
P [auth C],
R [auth C],
U [auth D],
V [auth D],
X [auth D]
PICEATANNOL
C14 H12 O4
CDRPUGZCRXZLFL-OWOJBTEDSA-N
BEZ
Query on BEZ

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B],
S [auth C],
Y [auth D]
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
L [auth B],
Q [auth C],
W [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CO (Subject of Investigation/LOI)
Query on CO

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
O [auth C],
T [auth D]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.05α = 90
b = 101.05β = 90
c = 448.184γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesEY009339
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesEY020551
Burroughs Wellcome FundUnited States1015187
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA157735
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM77387
Department of Veterans Affairs (VA, United States)United StatesBX002683

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Database references, Structure summary
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2022-04-13
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 2.0: 2023-02-08
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Experimental preparation, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-10-25
    Changes: Data collection