3EPM

Crystal structure of Caulobacter crescentus ThiC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.793 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily

Chatterjee, A.Li, Y.Zhang, Y.Grove, T.L.Lee, M.Krebs, C.Booker, S.J.Begley, T.P.Ealick, S.E.

(2008) Nat.Chem.Biol. 4: 758-765

  • DOI: 10.1038/nchembio.121
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 4-Amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase catalyzes a complex rearrangement of 5-aminoimidazole ribonucleotide (AIR) to form HMP-P, the pyrimidine moiety of thiamine phosphate. We determined the three-dimensional structure ...

    4-Amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase catalyzes a complex rearrangement of 5-aminoimidazole ribonucleotide (AIR) to form HMP-P, the pyrimidine moiety of thiamine phosphate. We determined the three-dimensional structures of HMP-P synthase and its complexes with the product HMP-P and a substrate analog imidazole ribotide. The structure of HMP-P synthase reveals a homodimer in which each protomer comprises three domains: an N-terminal domain with a novel fold, a central (betaalpha)(8) barrel and a disordered C-terminal domain that contains a conserved CX(2)CX(4)C motif, which is suggestive of a [4Fe-4S] cluster. Biochemical studies have confirmed that HMP-P synthase is iron sulfur cluster-dependent, that it is a new member of the radical SAM superfamily and that HMP-P and 5'-deoxyadenosine are products of the reaction. Mössbauer and EPR spectroscopy confirm the presence of one [4Fe-4S] cluster. Structural comparisons reveal that HMP-P synthase is homologous to a group of adenosylcobalamin radical enzymes. This similarity supports an evolutionary relationship between these two superfamilies.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, 120 Baker Laboratory, Cornell University, Ithaca, New York 14853-1301, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thiamine biosynthesis protein thiC
A, B
612Caulobacter vibrioides (strain ATCC 19089 / CB15)Mutation(s): 0 
Gene Names: thiC
EC: 4.1.99.17
Find proteins for Q9A6Q5 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Go to UniProtKB:  Q9A6Q5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HMH
Query on HMH

Download SDF File 
Download CCD File 
A
4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE
C6 H9 N3 O
VUTBELPREDJDDH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.793 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.247α = 90.00
b = 103.442β = 91.62
c = 95.369γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
DENZOdata reduction
ADSCdata collection
HKL-2000data reduction
MLPHAREphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description, Source and taxonomy