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 
  • R-Value Observed: 0.143 

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Ligand Structure Quality Assessment 


This is version 1.1 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.

(null) Nat Commun 6: 6480-6480

  • DOI: https://doi.org/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. 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, Texas A&M University, College Station, Texas 77843, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphomethylpyrimidine synthase, chloroplastic576Arabidopsis thalianaMutation(s): 0 
Gene Names: THICPY
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / 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
SF4
Query on SF4

Download Ideal Coordinates CCD File 
B [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
IRN
Query on IRN

Download Ideal Coordinates CCD File 
C [auth A]1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole
C8 H13 N2 O7 P
YEBULYOZZUNFGU-WCTZXXKLSA-N
BU1
Query on BU1

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.477α = 90
b = 107.477β = 90
c = 87.643γ = 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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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description