2FCT

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
syringomycin biosynthesis enzyme 2A, B313Pseudomonas syringae pv. syringaeMutation(s): 0 
Gene Names: syrB2
Find proteins for Q9RBY6 (Pseudomonas syringae pv. syringae)
Explore Q9RBY6 
Go to UniProtKB:  Q9RBY6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DSU
Query on DSU

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
AKG
Query on AKG

Download Ideal Coordinates CCD File 
G [auth A], K [auth B]2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
C [auth A], H [auth B]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], I [auth B], J [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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 = 57.15α = 90
b = 89.6β = 90
c = 124.89γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction
d*TREKdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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