1VLP

Crystal structure of a putative nicotinate phosphoribosyltransferase (yor209c, npt1) from saccharomyces cerevisiae at 1.75 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of a eukaryotic nicotinic acid phosphoribosyltransferase reveals structural heterogeneity among type II PRTases.

Chappie, J.S.Canaves, J.M.Han, G.W.Rife, C.L.Xu, Q.Stevens, R.C.

(2005) Structure 13: 1385-1396

  • DOI: 10.1016/j.str.2005.05.016
  • Primary Citation of Related Structures:  
    1VLP

  • PubMed Abstract: 
  • Nicotinamide adenine dinucleotide (NAD) is an essential cofactor for cellular redox reactions and can act as an important substrate in numerous biological processes. As a result, nature has evolved multiple biosynthetic pathways to meet this high chemical demand ...

    Nicotinamide adenine dinucleotide (NAD) is an essential cofactor for cellular redox reactions and can act as an important substrate in numerous biological processes. As a result, nature has evolved multiple biosynthetic pathways to meet this high chemical demand. In Saccharomyces cerevisiae, the NAD salvage pathway relies on the activity of nicotinic acid phosphoribosyltransferase (NAPRTase), a member of the phosphoribosyltransferase (PRTase) superfamily. Here, we report the structure of a eukaryotic (yeast) NAPRTase at 1.75 A resolution (locus name: YOR209C, gene name: NPT1). The structure reveals a two-domain fold that resembles the architecture of quinolinic acid phosphoribosyltransferases (QAPRTases), but with completely different dispositions that provide evidence for structural heterogeneity among the Type II PRTases. The identification of a third domain in NAPRTases provides a structural basis and possible mechanism for the functional modulation of this family of enzymes by ATP.


    Organizational Affiliation

    The Joint Center for Structural Genomics, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
nicotinate phosphoribosyltransferaseA, B, C, D441Saccharomyces cerevisiaeMutation(s): 9 
Gene Names: NPT1YOR209C
EC: 2.4.2.11 (PDB Primary Data), 6.3.4.21 (UniProt)
UniProt
Find proteins for P39683 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39683 
Go to UniProtKB:  P39683
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 1
  • Diffraction Data DOI: 10.18430/M31VLP Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.406α = 97.35
b = 83.103β = 95.67
c = 107.237γ = 97.99
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXCDphasing
SHARPphasing
REFMACrefinement
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-24
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description