Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 88.85 kDa 
• Atom Count: 5682 
• Modelled Residue Count: 713 
• Deposited Residue Count: 788 
• Unique protein chains: 1

3BU7

Crystal Structure and Biochemical Characterization of GDOsp, a Gentisate 1,2-Dioxygenase from Silicibacter Pomeroyi

• PDB DOI: 10.2210/pdb3BU7/pdb

• Classification: OXIDOREDUCTASE
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-02 Released: 2008-08-12 
• Deposition Author(s): Chen, J., Wang, M.Z., Zhu, G.Y., Zhang, X.C., Rao, Z.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.245 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Literature

Crystal structure and mutagenic analysis of GDOsp, a gentisate 1,2-dioxygenase from Silicibacter pomeroyi.

Chen, J., Li, W., Wang, M., Zhu, G., Liu, D., Sun, F., Hao, N., Li, X., Rao, Z., Zhang, X.C.

(2008) Protein Sci 17: 1362-1373

• PubMed: 18505738 
• DOI: 10.1110/ps.035881.108
• Primary Citation of Related Structures:  
  3BU7


• PubMed Abstract: 
  

Dioxygenases catalyze dioxygen incorporation into various organic compounds and play a key role in the complex degradation pathway of mono- and polycyclic aromatic and hetero-aromatic compounds. Here we report the crystal structure of gentisate 1,2-dioxygenase from Silicibacter pomeroyi (GDOsp) at a 2.8 A resolution. The enzyme possessed a conserved three-dimensional structure of the bicupin family, forming a homotetramerization. However, each subunit of GDOsp unusually contained two ferrous centers that were located in its two homologous cupin domains, respectively. Further mutagenic analysis indicated that the enzyme activity of GDOsp depends on the microenvironment in both metal-binding sites. Moreover, homologous structural comparison and functional study on GDOsp variants unveiled a group of functionally essential residues and suggested that the active site of the enzyme is located in the amino-terminal domain, but could be influenced by changes in the carboxyl domain. Therefore, GDOsp may provide a working model for studying long-distance communication within a protein (or its complex).

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gentisate 1,2-dioxygenase	A, B	394	N/A	Mutation(s): 0  Gene Names: gtdA-2 EC: 1.13.11.4
UniProt
Find proteins for Q5LLB1 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LLB1  Go to UniProtKB:  Q5LLB1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2	C [auth A], D [auth A], E [auth B], F [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.245 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.999	α = 90
b = 129.999	β = 90
c = 246.255	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-02 
• Released Date: 2008-08-12 
Deposition Author(s): Chen, J., Wang, M.Z., Zhu, G.Y., Zhang, X.C., Rao, Z.H.

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description