4S28

Crystal structure of Arabidopsis thaliana ThiC with bound aminoimidazole ribonucleotide, S-adenosylhomocysteine, Fe4S4 cluster and Fe

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.117 

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Literature

Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.

Fenwick, M.K., Mehta, A.P., Zhang, Y., Abdelwahed, S.H., Begley, T.P., Ealick, S.E.

(null) Nat Commun 6: 6480-6480

  • DOI: 10.1038/ncomms7480
  • Primary Citation of Related Structures:  
    4S25, 4S26, 4S27, 4S28, 4S29, 4S2A

  • PubMed Abstract: 

    • Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups ...

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

    Organizational Affiliation: 

    Department of Chemistry and Chemical Biology, Cornell University, 120 Baker Lab, Ithaca, New York 14853, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphomethylpyrimidine synthase, chloroplasticA576Arabidopsis thalianaMutation(s): 0 
Gene Names: THIC, PY, At2g29630, T27A16.27
EC: 4.1.99.17
UniProt
Find proteins for O82392 (Arabidopsis thaliana)
Explore O82392 
Go to UniProtKB:  O82392
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO82392
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH
Download Ideal Coordinates CCD File 
D [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N		 Ligand Interaction
SF4
Query on SF4
Download Ideal Coordinates CCD File 
B [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
AIR
Query on AIR
Download Ideal Coordinates CCD File 
C [auth A]5-AMINOIMIDAZOLE RIBONUCLEOTIDE
C8 H14 N3 O7 P
PDACUKOKVHBVHJ-XVFCMESISA-N		 Ligand Interaction
BU1
Query on BU1
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]		1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N		 Ligand Interaction
FE2
Query on FE2
Download Ideal Coordinates CCD File 
E [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.117 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.071α = 90
b = 107.071β = 90
c = 87.677γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release