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 1.4 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: https://doi.org/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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
nicotinate phosphoribosyltransferase
A, B, C, D
441Saccharomyces cerevisiaeMutation(s): 9 
Gene Names: NPT1YOR209C
EC: 2.4.2.11
UniProt
Find proteins for P39683 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39683 
Go to UniProtKB:  P39683
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39683
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
G [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
L [auth C],
O [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth B],
K [auth B],
N [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
M [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-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: https://doi.org/10.18430/M31VLP
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
  • Version 1.4: 2023-01-25
    Changes: Database references, Derived calculations