2BIW

Crystal structure of apocarotenoid cleavage oxygenase from Synechocystis, native enzyme

• PDB DOI: https://doi.org/10.2210/pdb2BIW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Synechocystis sp. PCC 6803
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-01-26 Released: 2005-04-14 
• Deposition Author(s): Kloer, D.P., Ruch, S., Al-Babili, S., Beyer, P., Schulz, G.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.224 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Starting Model: other

Literature

The Structure of a Retinal-Forming Carotenoid Oxygenase

Kloer, D.P., Ruch, S., Al-Babili, S., Beyer, P., Schulz, G.E.

(2005) Science 308: 267

• PubMed: 15821095 
• DOI: https://doi.org/10.1126/science.1108965
• Primary Citation of Related Structures:  
  2BIW, 2BIX


• PubMed Abstract: 
  

  Enzymes that produce retinal and related apocarotenoids constitute a sequence- and thus structure-related family, a member of which was analyzed by x-ray diffraction. This member is an oxygenase and contains an Fe2+-4-His arrangement at the axis of a seven-bladed beta-propeller chain fold covered by a dome formed by six large loops. The Fe2+ is accessible through a long nonpolar tunnel that holds a carotenoid derivative in one of the crystals. On binding, three consecutive double bonds of this carotenoid changed from a straight all-trans to a cranked cis-trans-cis conformation. The remaining trans bond is located at the dioxygen-ligated Fe2+ and cleaved by oxygen.

---

Organizational Affiliation: 

Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PQS (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 219.34 kDa 
• Atom Count: 15,742 
• Modelled Residue Count: 1,916 
• Deposited Residue Count: 1,960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APOCAROTENOID-CLEAVING OXYGENASE	A, B, C, D	490	Synechocystis sp. PCC 6803	Mutation(s): 0  EC: 1.13.11.75
UniProt
Find proteins for P74334 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P74334  Go to UniProtKB:  P74334

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3ON	E [auth A], G [auth B], I [auth C], K [auth D]	(3R)-3-HYDROXY-8'-APOCAROTENOL C30 H42 O2 FNAJVVMDXCOSFY-VFGOXHQXSA-N
FE	F [auth A], H [auth B], J [auth C], L [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.224 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.046	α = 90
b = 125.278	β = 90
c = 203.086	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-14 
Deposition Author(s): Kloer, D.P., Ruch, S., Al-Babili, S., Beyer, P., Schulz, G.E.

Revision History  

• Version 1.0: 2005-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description