Crystal Structure of T.th. HB8 CTP synthetase complex with Glutamine

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.236 

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This is version 1.3 of the entry. See complete history


Crystal Structures of CTP Synthetase Reveal ATP, UTP, and Glutamine Binding Sites

Goto, M.Omi, R.Nakagawa, N.Miyahara, I.Hirotsu, K.

(2004) Structure 12: 1413-1423

  • DOI: https://doi.org/10.1016/j.str.2004.05.013
  • Primary Citation of Related Structures:  
    1VCM, 1VCN, 1VCO

  • PubMed Abstract: 

    CTP synthetase (CTPs) catalyzes the last step in CTP biosynthesis, in which ammonia generated at the glutaminase domain reacts with the ATP-phosphorylated UTP at the synthetase domain to give CTP. Glutamine hydrolysis is active in the presence of ATP and UTP and is stimulated by the addition of GTP. We report the crystal structures of Thermus thermophilus HB8 CTPs alone, CTPs with 3SO4(2-), and CTPs with glutamine. The enzyme is folded into a homotetramer with a cross-shaped structure. Based on the binding mode of sulfate anions to the synthetase site, ATP and UTP are computer modeled into CTPs with a geometry favorable for the reaction. Glutamine bound to the glutaminase domain is situated next to the triad of Glu-His-Cys as a catalyst and a water molecule. Structural information provides an insight into the conformational changes associated with the binding of ATP and UTP and the formation of the GTP binding site.

  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CTP synthetase550Thermus thermophilusMutation(s): 0 
Gene Names: HB8
Find proteins for Q5SIA8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIA8 
Go to UniProtKB:  Q5SIA8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIA8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GLN

Download Ideal Coordinates CCD File 
C5 H10 N2 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.236 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.73α = 90
b = 120.88β = 90
c = 143.32γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations