2Y8N

Crystal structure of glycyl radical enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis for a Kolbe-Type Decarboxylation Catalyzed by a Glycyl Radical Enzyme.

Martins, B.M.Blaser, M.Feliks, M.Ullmann, G.M.Buckel, W.Selmer, T.

(2011) J Am Chem Soc 133: 14666

  • DOI: 10.1021/ja203344x
  • Primary Citation of Related Structures:  
    2Y8N, 2YAJ

  • PubMed Abstract: 
  • 4-Hydroxyphenylacetate decarboxylase is a [4Fe-4S] cluster containing glycyl radical enzyme proposed to use a glycyl/thiyl radical dyad to catalyze the last step of tyrosine fermentation in clostridia. The decarboxylation product p-cresol (4-methylphenol) is a virulence factor of the human pathogen Clostridium difficile ...

    4-Hydroxyphenylacetate decarboxylase is a [4Fe-4S] cluster containing glycyl radical enzyme proposed to use a glycyl/thiyl radical dyad to catalyze the last step of tyrosine fermentation in clostridia. The decarboxylation product p-cresol (4-methylphenol) is a virulence factor of the human pathogen Clostridium difficile . Here we describe the crystal structures at 1.75 and 1.81 Å resolution of substrate-free and substrate-bound 4-hydroxyphenylacetate decarboxylase from the related Clostridium scatologenes . The structures show a (βγ)(4) tetramer of heterodimers composed of a catalytic β-subunit harboring the putative glycyl/thiyl dyad and a distinct small γ-subunit with two [4Fe-4S] clusters at 40 Å distance from the active site. The γ-subunit comprises two domains displaying pseudo-2-fold symmetry that are structurally related to the [4Fe-4S] cluster-binding scaffold of high-potential iron-sulfur proteins. The N-terminal domain coordinates one cluster with one histidine and three cysteines, and the C-terminal domain coordinates the second cluster with four cysteines. Whereas the C-terminal cluster is buried in the βγ heterodimer interface, the N-terminal cluster is not part of the interface. The previously postulated decarboxylation mechanism required the substrate's hydroxyl group in the vicinity of the active cysteine residue. In contrast to expectation, the substrate-bound state shows a direct interaction between the substrate's carboxyl group and the active site Cys503, while His536 and Glu637 at the opposite side of the active site pocket anchor the hydroxyl group. This state captures a possible catalytically competent complex and suggests a Kolbe-type decarboxylation for p-cresol formation.


    Organizational Affiliation

    Institute für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, D-10115 Berlin, Germany. berta.martins@biologie.hu-berlin.de



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNITA, C897Clostridium scatologenesMutation(s): 0 
Gene Names: csdB
EC: 4.1.1.83
UniProt
Find proteins for Q38HX4 (Clostridium scatologenes)
Explore Q38HX4 
Go to UniProtKB:  Q38HX4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38HX4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNITB, D86Clostridium scatologenesMutation(s): 0 
Gene Names: csdC
EC: 4.1.1.83
UniProt
Find proteins for Q38HX3 (Clostridium scatologenes)
Explore Q38HX3 
Go to UniProtKB:  Q38HX3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38HX3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B],
G [auth D],
H [auth D]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.28α = 90
b = 227.76β = 90
c = 148.01γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
AMoREphasing
SHARPphasing
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-10-19
    Changes: Database references
  • Version 1.2: 2017-07-05
    Changes: Data collection
  • Version 1.3: 2019-10-16
    Changes: Data collection, Experimental preparation, Other