Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.57 kDa 
• Atom Count: 3072 
• Modelled Residue Count: 356 
• Deposited Residue Count: 356 
• Unique protein chains: 1

3NR1

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

• DOI: 10.2210/pdb3NR1/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-30 Released: 2010-09-08 
• Deposition Author(s): Sun, D.W., Kim, H.Y., Kim, K.J., Jeon, Y.H., Chung, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.230 
• R-Value Work: 0.203 

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

• PubMed: 20818390 
• DOI: 10.1038/nsmb.1906
• Primary Citation of Related Structures:  
  3NQW, 3NR1


• 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) 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HD domain-containing protein 3	A, B	178	Homo sapiens	Mutation(s): 0  Gene Names: HDDC3, MESH1 EC: 3.1.7.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N4P3 (Homo sapiens) Explore Q8N4P3  Go to UniProtKB:  Q8N4P3
PHAROS:  Q8N4P3 GTEx:  ENSG00000184508

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], D [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.230 
• R-Value Work: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.9	α = 90
b = 62.4	β = 95.3
c = 53.9	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-30 
• Released Date: 2010-09-08 
Deposition Author(s): Sun, D.W., Kim, H.Y., Kim, K.J., Jeon, Y.H., Chung, J.

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