Crystal structure of Caulobacter crescentus ThiC complexed with HMP-P

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.156 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1038/nchembio.121
  • Primary Citation of Related Structures:  
    3EPM, 3EPN, 3EPO

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiamine biosynthesis protein thiC
A, B
612Caulobacter vibrioidesMutation(s): 0 
Find proteins for Q9A6Q5 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Explore Q9A6Q5 
Go to UniProtKB:  Q9A6Q5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9A6Q5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MP5

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C6 H10 N3 O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.021α = 90
b = 103.193β = 102.17
c = 83.105γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references