3EC1 | pdb_00003ec1

Structure of YqeH GTPase from Geobacillus stearothermophilus (an AtNOS1 / AtNOA1 ortholog)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.287 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.254 (Depositor), 0.230 (DCC) 

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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

The structure of YqeH. An AtNOS1/AtNOA1 ortholog that couples GTP hydrolysis to molecular recognition.

Sudhamsu, J.Lee, G.I.Klessig, D.F.Crane, B.R.

(2008) J Biological Chem 283: 32968-32976

  • DOI: https://doi.org/10.1074/jbc.M804837200
  • Primary Citation of Related Structures:  
    3EC1

  • PubMed Abstract: 

    AtNOS1/AtNOA1 was identified as a nitric oxide-generating enzyme in plants, but that function has recently been questioned. To resolve issues surrounding AtNOA1 activity, we report the biochemical properties and a 2.36 A resolution crystal structure of a bacterial AtNOA1 ortholog (YqeH). Geobacillus YqeH fused to a putative AtNOA1 leader peptide complements growth and morphological defects of Atnoa1 mutant plants. YqeH does not synthesize nitric oxide from L-arginine but rather hydrolyzes GTP. The YqeH structure reveals a circularly permuted GTPase domain and an unusual C-terminal beta-domain. A small N-terminal domain, disordered in the structure, binds zinc. Structural homology among the C-terminal domain, the RNA-binding regulator TRAP, and the hypoxia factor pVHL define a recognition module for peptides and nucleic acids. TRAP residues important for RNA binding are conserved by the YqeH C-terminal domain, whose positioning is coupled to GTP hydrolysis. YqeH and AtNOA1 probably act as G-proteins that regulate nucleic acid recognition and not as nitric-oxide synthases.


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein YqeH required for biosis of 30S ribosome subunit
A, B
369Geobacillus stearothermophilusMutation(s): 0 
Gene Names: yqeHB4114_2212D9548_03520TGS27_0162
UniProt
Find proteins for D0VWU7 (Geobacillus stearothermophilus)
Explore D0VWU7 
Go to UniProtKB:  D0VWU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWU7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.287 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.254 (Depositor), 0.230 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.615α = 90
b = 81.097β = 91.5
c = 108.173γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GDPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-06-24
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations