5U8X | pdb_00005u8x

Crystal structure of Fe-CAO1

  • 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), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Burroughs Wellcome Fund, Department of Veterans Affairs (VA, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.205 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5U8X

This is version 3.0 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 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.

Macromolecule Content 

  • Total Structure Weight: 238.72 kDa 
  • Atom Count: 17,168 
  • Modeled Residue Count: 1,991 
  • Deposited Residue Count: 2,104 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BEZ

Query on BEZ



Download:Ideal Coordinates CCD File
I [auth B],
L [auth C],
O [auth D]
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
FE2
(Subject of Investigation/LOI)

Query on FE2



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
J [auth C],
M [auth D]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
K [auth C],
N [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.205 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.181 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.908α = 90
b = 100.908β = 90
c = 448.815γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
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
Burroughs Wellcome FundUnited States1015187
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: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 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, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-10-25
    Changes: Data collection
  • Version 3.0: 2024-07-10
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Refinement description, Structure summary