3NR1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.203 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HD domain-containing protein 3
A, B
178Homo sapiensGene Names: HDDC3 (MESH1)
EC: 3.1.7.2
Find proteins for Q8N4P3 (Homo sapiens)
Go to Gene View: HDDC3
Go to UniProtKB:  Q8N4P3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.900α = 90.00
b = 62.400β = 95.30
c = 53.900γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
RESOLVEphasing
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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