4OGW

Structure of a human CD38 mutant complexed with NMN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A pre-steady state and steady state kinetic analysis of the N-ribosyl hydrolase activity of hCD157.

Preugschat, F.Carter, L.H.Boros, E.E.Porter, D.J.Stewart, E.L.Shewchuk, L.M.

(2014) Arch Biochem Biophys 564C: 156-163

  • DOI: https://doi.org/10.1016/j.abb.2014.09.008
  • Primary Citation of Related Structures:  
    4OGW

  • PubMed Abstract: 

    hCD157 catalyzes the hydrolysis of nicotinamide riboside (NR) and nicotinic acid riboside (NAR). The release of nicotinamide or nicotinic acid from NR or NAR was confirmed by spectrophotometric, HPLC and NMR analyses. hCD157 is inactivated by a mechanism-based inhibitor, 2'-deoxy-2'-fluoro-nicotinamide arabinoside (fNR). Modification of the enzyme during the catalytic cycle by NR, NAR, or fNR increased the intrinsic protein fluorescence by approximately 50%. Pre-steady state and steady state data were used to derive a minimal kinetic scheme for the hydrolysis of NR. After initial complex formation a reversible step (360 and 30s(-1)) is followed by a slow irreversible step (0.1s(-1)) that defined the rate limiting step, or kcat. The calculated KMapp value for NR in the hydrolytic reaction is 6nM. The values of the kinetic constants suggest that one biological function of cell-surface hCD157 is to bind and slowly hydrolyze NR, possibly converting it to a ligand-activated receptor. Differences in substrate preference between hCD157 and hCD38 were rationalized through a comparison of the crystal structures of the two proteins. This comparison identified several residues in hCD157 (F108 and F173) that can potentially hinder the binding of dinucleotide substrates (NAD+).


  • Organizational Affiliation

    Muscle Metabolism Discovery Performance Unit, GlaxoSmithKline, 5 Moore Drive, 3.2094, Research Triangle Park, NC 27709, United States. Electronic address: Frank.X.Preugschat@gsk.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosyl cyclase 1257Homo sapiensMutation(s): 5 
Gene Names: CD38
EC: 3.2.2.5 (PDB Primary Data), 3.2.2 (UniProt), 3.2.2.6 (UniProt), 2.4.99.20 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P28907 (Homo sapiens)
Explore P28907 
Go to UniProtKB:  P28907
PHAROS:  P28907
GTEx:  ENSG00000004468 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28907
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NMN
Query on NMN

Download Ideal Coordinates CCD File 
B [auth A]BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
C11 H16 N2 O8 P
DAYLJWODMCOQEW-TURQNECASA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.341α = 90
b = 64.467β = 90
c = 73.501γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary