Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 72.41 kDa 
• Atom Count: 5412 
• Modelled Residue Count: 603 
• Deposited Residue Count: 626 
• Unique protein chains: 1

2FCT

SyrB2 with Fe(II), chloride, and alpha-ketoglutarate

• PDB DOI: 10.2210/pdb2FCT/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Pseudomonas syringae pv. syringae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-12-12 Released: 2006-03-21 
• Deposition Author(s): Blasiak, L.C., Drennan, C.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.204 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

Crystal structure of the non-haem iron halogenase SyrB2 in syringomycin biosynthesis.

Blasiak, L.C., Vaillancourt, F.H., Walsh, C.T., Drennan, C.L.

(2006) Nature 440: 368-371

• PubMed: 16541079 
• DOI: 10.1038/nature04544
• Primary Citation of Related Structures:  
  2FCT, 2FCU, 2FCV


• PubMed Abstract: 
  

Non-haem Fe(II)/alpha-ketoglutarate (alphaKG)-dependent enzymes harness the reducing power of alphaKG to catalyse oxidative reactions, usually the hydroxylation of unactivated carbons, and are involved in processes such as natural product biosynthesis, the mammalian hypoxic response, and DNA repair. These enzymes couple the decarboxylation of alphaKG with the formation of a high-energy ferryl-oxo intermediate that acts as a hydrogen-abstracting species. All previously structurally characterized mononuclear iron enzymes contain a 2-His, 1-carboxylate motif that coordinates the iron. The two histidines and one carboxylate, known as the 'facial triad', form one triangular side of an octahedral iron coordination geometry. A subclass of mononuclear iron enzymes has been shown to catalyse halogenation reactions, rather than the more typical hydroxylation reaction. SyrB2, a member of this subclass, is a non-haem Fe(II)/alphaKG-dependent halogenase that catalyses the chlorination of threonine in syringomycin E biosynthesis. Here we report the structure of SyrB2 with both a chloride ion and alphaKG coordinated to the iron ion at 1.6 A resolution. This structure reveals a previously unknown coordination of iron, in which the carboxylate ligand of the facial triad is replaced by a chloride ion.

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Organizational Affiliation: 

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
syringomycin biosynthesis enzyme 2	A, B	313	Pseudomonas syringae pv. syringae	Mutation(s): 0  Gene Names: syrB2
UniProt
Find proteins for Q9RBY6 (Pseudomonas syringae pv. syringae) Explore Q9RBY6  Go to UniProtKB:  Q9RBY6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DSU	F [auth A]	((2R,3S,4S,5S)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)-5-((2R,3S,4S,5S,6R)-3,4,5-TRIHYDROXY-6-METHOXY-TETRAHYDRO-2H-PYRAN-2-YLOXY)-TETRAHYDROFURAN-2-YL)METHYL NONANOATE C22 H40 O12 GCKKEFVHVGTJPT-PZOSHJPSSA-N
AKG	G [auth A], K [auth B]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE2	C [auth A], H [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CL	D [auth A], E [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.204 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.15	α = 90
b = 89.6	β = 90
c = 124.89	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
d*TREK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-12-12 
• Released Date: 2006-03-21 
Deposition Author(s): Blasiak, L.C., Drennan, C.L.

Revision History  

• Version 1.0: 2006-03-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance