Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 40.97 kDa 
• Atom Count: 2697 
• Residue Count: 339 
• Unique protein chains: 2

1HL3

CtBP/BARS in ternary complex with NAD(H) and PIDLSKK peptide

• DOI: 10.2210/pdb1HL3/pdb

• Classification: TRANCRIPTION CO-REPRESSOR
• Organism(s): Rattus norvegicus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-03-13 Released: 2003-06-19 
• Deposition Author(s): Nardini, M., Spano, S., Cericola, C., Pesce, A., Massaro, A., Millo, E., Luini, A., Corda, D., Bolognesi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.315 
• R-Value Work: 0.256 
• R-Value Observed: 0.256 

Literature

Ctbp/Bars: A Dual-Function Protein Involved in Transcription Co-Repression and Golgi Membrane Fission

Nardini, M., Spano, S., Cericola, C., Pesce, A., Massaro, A., Millo, E., Luini, A., Corda, D., Bolognesi, M.

(2003) EMBO J 22: 3122

• PubMed: 12805226 
• DOI: 10.1093/emboj/cdg283
• Primary Citation of Related Structures:  
  1HL3, 1HKU


• PubMed Abstract: 
  

C-terminal-binding protein/brefeldin A-ADP ribosylated substrate (CtBP/BARS) plays key roles in development and oncogenesis as a transcription co-repressor, and in intracellular traffic as a promoter of Golgi membrane fission. Co-repressor activity is regulated by NAD(H) binding to CtBP/BARS, while membrane fission is associated with its acyl-CoA-dependent acyltransferase activity. Here, we report the crystal structures of rat CtBP/BARS in a binary complex with NAD(H), and in a ternary complex with a PIDLSKK peptide mimicking the consensus motif (PXDLS) recognized in CtBP/BARS cellular partners. The structural data show CtBP/BARS in a NAD(H)-bound dimeric form; the peptide binding maps the recognition site for DNA-binding proteins and histone deacetylases to an N-terminal region of the protein. The crystal structure together with the site-directed mutagenesis data and binding experiments suggest a rationale for the molecular mechanisms underlying the two fundamental co-existing, but diverse, activities supported by CtBP/BARS in the nucleus and in Golgi membranes.

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Related Citations: 

• Crystallization and Preliminary X-Ray Diffraction Analysis of Brefeldin A-Adp Ribosylated Substrate (Bars)
  Nardini, M., Spano, S., Cericola, C., Pesce, A., Damonte, G., Luini, A., Corda, D., Bolognesi, M.
  (2002) Acta Crystallogr D Biol Crystallogr D58: 1068

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Organizational Affiliation: 

Department of Physics-INFM, University of Genova, Via Dodecaneso 33, 16146 Genova, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-TERMINAL BINDING PROTEIN 3	A	358	Rattus norvegicus	Mutation(s): 0  Gene Names: Ctbp1, Bars, Ctbp3 EC: 1.1.1
Find proteins for Q9Z2F5 (Rattus norvegicus) Explore Q9Z2F5  Go to UniProtKB:  Q9Z2F5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PRO-ILE-ASP-LEU-SER-LYS-LYS PEPTIDE	B	7	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	A	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.315 
• R-Value Work: 0.256 
• R-Value Observed: 0.256 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.811	α = 90
b = 84.811	β = 90
c = 159.719	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-03-13 
• Released Date: 2003-06-19 
Deposition Author(s): Nardini, M., Spano, S., Cericola, C., Pesce, A., Massaro, A., Millo, E., Luini, A., Corda, D., Bolognesi, M.

Revision History 

• Version 1.0: 2003-06-19
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance