6BIG | pdb_00006big

Crystal structure of cobalt-substituted Synechocystis ACO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 
    0.229 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history

Literature

Preparation and characterization of metal-substituted carotenoid cleavage oxygenases.

Sui, X.Farquhar, E.R.Hill, H.E.von Lintig, J.Shi, W.Kiser, P.D.

(2018) J Biol Inorg Chem 23: 887-901

  • DOI: https://doi.org/10.1007/s00775-018-1586-0
  • Primary Citation Related Structures: 
    6B86, 6BIG

  • PubMed Abstract: 

    Carotenoid cleavage oxygenases (CCO) are non-heme iron enzymes that catalyze oxidative cleavage of alkene bonds in carotenoid and stilbenoid substrates. Previously, we showed that the iron cofactor of CAO1, a resveratrol-cleaving member of this family, can be substituted with cobalt to yield a catalytically inert enzyme useful for trapping active site-bound stilbenoid substrates for structural characterization. Metal substitution may provide a general method for identifying the natural substrates for CCOs in addition to facilitating structural and biophysical characterization of CCO-carotenoid complexes under normal aerobic conditions. Here, we demonstrate the general applicability of cobalt substitution in a prototypical carotenoid cleaving CCO, apocarotenoid oxygenase (ACO) from Synechocystis. Among the non-native divalent metals investigated, cobalt was uniquely able to stably occupy the ACO metal binding site and inhibit catalysis. Analysis by X-ray crystallography and X-ray absorption spectroscopy demonstrate that the Co(II) forms of both ACO and CAO1 exhibit a close structural correspondence to the native Fe(II) enzyme forms. Hence, cobalt substitution is an effective strategy for generating catalytically inert but structurally intact forms of CCOs.


  • Organizational Affiliation
    • Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, USA.

Macromolecule Content 

  • Total Structure Weight: 217.72 kDa 
  • Atom Count: 15,788 
  • Modeled Residue Count: 1,916 
  • Deposited Residue Count: 1,960 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Apocarotenoid-15,15'-oxygenase
A, B, C, D
490Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: sll1541
EC: 1.13.11.75
UniProt
Find proteins for P74334 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P74334 
Go to UniProtKB:  P74334
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP74334
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free:  0.229 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.074α = 90
b = 124.531β = 90
c = 202.608γ = 90
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  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description