Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 101.37 kDa 
• Atom Count: 6708 
• Residue Count: 822 
• Unique protein chains: 1

1EMS

CRYSTAL STRUCTURE OF THE C. ELEGANS NITFHIT PROTEIN

• DOI: 10.2210/pdb1EMS/pdb

• Classification: ANTITUMOR PROTEIN
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-03-17 Released: 2000-07-20 
• Deposition Author(s): Pace, H.C., Hodawadekar, S.C., Draganescu, A., Huang, J., Bieganowski, P., Pekarsky, Y., Croce, C.M., Brenner, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.231 
• R-Value Work: 0.190 
• R-Value Observed: 0.181 

Literature

Crystal structure of the worm NitFhit Rosetta Stone protein reveals a Nit tetramer binding two Fhit dimers.

Pace, H.C., Hodawadekar, S.C., Draganescu, A., Huang, J., Bieganowski, P., Pekarsky, Y., Croce, C.M., Brenner, C.

(2000) Curr Biol 10: 907-917

• PubMed: 10959838 
• DOI: 10.1016/s0960-9822(00)00621-7
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The nucleotide-binding protein Fhit, among the earliest and most frequently inactivated proteins in lung cancer, suppresses tumor formation by inducing apoptosis. In invertebrates, Fhit is encoded as a fusion protein with Nit, a member of the nitrilase superfamily. In mice, the Nit1 and Fhit genes have nearly identical expression profiles. According to the Rosetta Stone hypothesis, if the separate Nit and Fhit genes could be shown to occur in the same subset of genomes (that is, to share a phylogenetic profile), then the existence of a fusion protein in invertebrates and the coordinated expression of separate mRNAs in mouse suggest that Nit and Fhit function in the same pathway and that the structure of invertebrate NitFhit may reflect the nature of Nit-Fhit interactions.

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Related Citations: 

• Nitrilase and Fhit homologs are encoded as fusion proteins in Drosophila melanogaster and Caenorhabditis elegans
  Pekarsky, Y., Campiglio, M., Siprashvili, Z., Druck, T., Sedkov, Y., Tillib, S., Draganescu, A., Wermuth, P., Rothman, J.H., Huebner, K., Buchberg, A.M., Mazo, A., Brenner, C., Croce, C.M.
  (1998) Proc Natl Acad Sci U S A 95: 8744

• Genetic, biochemical and crystallographic characterization of Fhit-substrate complexes as the active signaling form of Fhit
  Pace, H.C., Garrison, P.N., Robinson, A.K., Barnes, L.D., Draganescu, A., Rosler, A., Blackburn, G.M., Siprashvili, Z., Croce, C.M., Huebner, K., Brenner, C.
  (1998) Proc Natl Acad Sci U S A 95: 5484

• The Histidine Triad Superfamily of Nucleotide-Binding Proteins
  Brenner, C., Bieganowski, P., Pace, H.C., Huebner, K.
  (1999) J Cell Physiol 181: 179

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Organizational Affiliation: 

Structural Biology and Bioinformatics Program, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NIT-FRAGILE HISTIDINE TRIAD FUSION PROTEIN	A, B	440	Caenorhabditis elegans	Mutation(s): 0  Gene Names: nft-1, Y56A3A.13 EC: 3.6.1.29 (UniProt), 3.5 (UniProt)
Find proteins for O76463 (Caenorhabditis elegans) Go to UniProtKB:  O76463

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EMC	A, B	ETHYL MERCURY ION C2 H5 Hg MJOUBOKSWBMNGQ-UHFFFAOYSA-N
MPD	A	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
NA	A, B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.231 
• R-Value Work: 0.190 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.75	α = 90
b = 100.44	β = 90
c = 158.65	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-03-17 
• Released Date: 2000-07-20 
Deposition Author(s): Pace, H.C., Hodawadekar, S.C., Draganescu, A., Huang, J., Bieganowski, P., Pekarsky, Y., Croce, C.M., Brenner, C.

Revision History 

• Version 1.0: 2000-07-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance