4CYF

The structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

The Structure of Vanin-1: A Key Enzyme Linking Metabolic Disease and Inflammation

Boersma, Y.L.Newman, J.Adams, T.E.Cowieson, N.Krippner, G.Bozaoglu, K.Peat, T.S.

(2014) Acta Crystallogr.,Sect.D 70: 3320

  • DOI: 10.1107/S1399004714022767
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although part of the coenzyme A pathway, vanin 1 (also known as pantetheinase) sits on the cell surface of many cell types as an ectoenzyme, catalyzing the breakdown of pantetheine to pantothenic acid (vitamin B5) and cysteamine, a strong reducing ag ...

    Although part of the coenzyme A pathway, vanin 1 (also known as pantetheinase) sits on the cell surface of many cell types as an ectoenzyme, catalyzing the breakdown of pantetheine to pantothenic acid (vitamin B5) and cysteamine, a strong reducing agent. Vanin 1 was initially discovered as a protein involved in the homing of leukocytes to the thymus. Numerous studies have shown that vanin 1 is involved in inflammation, and more recent studies have shown a key role in metabolic disease. Here, the X-ray crystal structure of human vanin 1 at 2.25 Å resolution is presented, which is the first reported structure from the vanin family, as well as a crystal structure of vanin 1 bound to a specific inhibitor. These structures illuminate how vanin 1 can mediate its biological roles by way of both enzymatic activity and protein-protein interactions. Furthermore, it sheds light on how the enzymatic activity is regulated by a novel allosteric mechanism at a domain interface.


    Organizational Affiliation

    Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PANTETHEINASE
A, B
506Homo sapiensMutation(s): 0 
Gene Names: VNN1
EC: 3.5.1.92
Find proteins for O95497 (Homo sapiens)
Go to Gene View: VNN1
Go to UniProtKB:  O95497
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 119.941α = 90.00
b = 119.941β = 90.00
c = 221.887γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
Auto-Rickshawphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references
  • Version 2.0: 2017-06-14
    Type: Advisory, Atomic model, Derived calculations
  • Version 2.1: 2019-05-08
    Type: Data collection, Experimental preparation