4S25

Crystal structure of Arabidopsis thaliana ThiC with bound imidazole ribonucleotide, S-adenosylhomocysteine, Fe4S4 cluster and Zn (trigonal crystal form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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.

(--) Nat Commun 6: 6480-6480

  • DOI: 10.1038/ncomms7480
  • Primary Citation of Related Structures:  

  • 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 loca ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphomethylpyrimidine synthase, chloroplastic
A
576Arabidopsis thalianaMutation(s): 0 
Gene Names: THIC (PY)
EC: 4.1.99.17
Find proteins for O82392 (Arabidopsis thaliana)
Go to UniProtKB:  O82392
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BU1
Query on BU1

Download SDF File 
Download CCD File 
A
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
IRN
Query on IRN

Download SDF File 
Download CCD File 
A
1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole
C8 H13 N2 O7 P
YEBULYOZZUNFGU-WCTZXXKLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.142 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 107.477α = 90.00
b = 107.477β = 90.00
c = 87.643γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
PHENIXrefinement
PHENIXphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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