2YWR

Crystal structure of GAR transformylase from Aquifex aeolicus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures and reaction mechanisms of the two related enzymes, PurN and PurU.

Sampei, G.Kanagawa, M.Baba, S.Shimasaki, T.Taka, H.Mitsui, S.Fujiwara, S.Yanagida, Y.Kusano, M.Suzuki, S.Terao, K.Kawai, H.Fukai, Y.Nakagawa, N.Ebihara, A.Kuramitsu, S.Yokoyama, S.Kawai, G.

(2013) J.Biochem. 154: 569-579

  • DOI: 10.1093/jb/mvt090
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of glycinamide ribonucleotide transformylases (PurNs) from Aquifex aeolicus (Aa), Geobacillus kaustophilus (Gk) and Symbiobacterium toebii (St), and of formyltetrahydrofolate hydrolase (PurU) from Thermus thermophilus (Tt) were ...

    The crystal structures of glycinamide ribonucleotide transformylases (PurNs) from Aquifex aeolicus (Aa), Geobacillus kaustophilus (Gk) and Symbiobacterium toebii (St), and of formyltetrahydrofolate hydrolase (PurU) from Thermus thermophilus (Tt) were determined. The monomer structures of the determined PurN and PurU were very similar to the known structure of PurN, but oligomeric states were different; AaPurN and StPurN formed dimers, GkPurN formed monomer and PurU formed tetramer in the crystals. PurU had a regulatory ACT domain in its N-terminal side. So far several structures of PurUs have been determined, yet, the mechanisms of the catalysis and the regulation of PurU have not been elucidated. We, therefore, modelled ligand-bound structures of PurN and PurU, and performed molecular dynamics simulations to elucidate the reaction mechanisms. The evolutionary relationship of the two enzymes is discussed based on the comparisons of the structures and the catalytic mechanisms.


    Organizational Affiliation

    Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan; RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan; Structural Biology Group, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5198, Japan; Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan; and Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoribosylglycinamide formyltransferase
A
216Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: purN
EC: 2.1.2.2
Find proteins for O67023 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67023
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.204 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.955α = 90.00
b = 59.955β = 90.00
c = 105.934γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOLREPphasing
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-01-15
    Type: Database references