3NQW

A metazoan ortholog of SpoT hydrolyzes ppGpp and plays a role in starvation responses


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses

Sun, D.W.Lee, G.Lee, J.H.Kim, H.Y.Rhee, H.W.Park, S.Y.Kim, K.J.Kim, Y.Kim, B.Y.Hong, J.I.Park, C.Choy, H.E.Kim, J.H.Jeon, Y.H.Chung, J.

(2010) Nat Struct Mol Biol 17: 1188-1194

  • DOI: 10.1038/nsmb.1906
  • Primary Citation of Related Structures:  
    3NR1, 3NQW

  • PubMed Abstract: 
  • In nutrient-starved bacteria, RelA and SpoT proteins have key roles in reducing cell growth and overcoming stresses. Here we identify functional SpoT orthologs in metazoa (named Mesh1, encoded by HDDC3 in human and Q9VAM9 in Drosophila melanogaster) ...

    In nutrient-starved bacteria, RelA and SpoT proteins have key roles in reducing cell growth and overcoming stresses. Here we identify functional SpoT orthologs in metazoa (named Mesh1, encoded by HDDC3 in human and Q9VAM9 in Drosophila melanogaster) and reveal their structures and functions. Like the bacterial enzyme, Mesh1 proteins contain an active site for ppGpp hydrolysis and a conserved His-Asp-box motif for Mn(2+) binding. Consistent with these structural data, Mesh1 efficiently catalyzes hydrolysis of guanosine 3',5'-diphosphate (ppGpp) both in vitro and in vivo. Mesh1 also suppresses SpoT-deficient lethality and RelA-induced delayed cell growth in bacteria. Notably, deletion of Mesh1 (Q9VAM9) in Drosophila induces retarded body growth and impaired starvation resistance. Microarray analyses reveal that the amino acid-starved Mesh1 null mutant has highly downregulated DNA and protein synthesis-related genes and upregulated stress-responsible genes. These data suggest that metazoan SpoT orthologs have an evolutionarily conserved function in starvation responses.


    Organizational Affiliation

    Division of Magnetic Resonance, Korea Basic Science Institute, Chungbuk, South Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CG11900AB179Drosophila melanogasterMutation(s): 0 
Gene Names: CG11900Dmel_CG11900Mesh1
EC: 3.1.7.2
Find proteins for Q9VAM9 (Drosophila melanogaster)
Explore Q9VAM9 
Go to UniProtKB:  Q9VAM9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50α = 90
b = 71.4β = 101.4
c = 49.9γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-10-09
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description