6DE1 | pdb_00006de1

Crystal structure of the single mutant (D52N) of the full-length NT5C2 in the active state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6DE1

This is version 1.3 of the entry. See complete history

Literature

Structure and Mechanisms of NT5C2 Mutations Driving Thiopurine Resistance in Relapsed Lymphoblastic Leukemia.

Dieck, C.L.Tzoneva, G.Forouhar, F.Carpenter, Z.Ambesi-Impiombato, A.Sanchez-Martin, M.Kirschner-Schwabe, R.Lew, S.Seetharaman, J.Tong, L.Ferrando, A.A.

(2018) Cancer Cell 34: 136-147.e6

  • DOI: https://doi.org/10.1016/j.ccell.2018.06.003
  • Primary Citation Related Structures: 
    6DD3, 6DDB, 6DDC, 6DDH, 6DDK, 6DDL, 6DDO, 6DDQ, 6DDX, 6DDY, 6DDZ, 6DE0, 6DE1, 6DE2, 6DE3

  • PubMed Abstract: 

    Activating mutations in the cytosolic 5'-nucleotidase II gene NT5C2 drive resistance to 6-mercaptopurine in acute lymphoblastic leukemia. Here we demonstrate that constitutively active NT5C2 mutations K359Q and L375F reconfigure the catalytic center for substrate access and catalysis in the absence of allosteric activator. In contrast, most relapse-associated mutations, which involve the arm segment and residues along the surface of the inter-monomeric cavity, disrupt a built-in switch-off mechanism responsible for turning off NT5C2. In addition, we show that the C-terminal acidic tail lost in the Q523X mutation functions to restrain NT5C2 activation. These results uncover dynamic mechanisms of enzyme regulation targeted by chemotherapy resistance-driving NT5C2 mutations, with important implications for the development of NT5C2 inhibitor therapies.


  • Organizational Affiliation
    • Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.

Macromolecule Content 

  • Total Structure Weight: 67.43 kDa 
  • Atom Count: 4,119 
  • Modeled Residue Count: 467 
  • Deposited Residue Count: 579 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytosolic purine 5'-nucleotidase579Homo sapiensMutation(s): 1 
Gene Names: NT5C2NT5BNT5CPPNT5
EC: 3.1.3.5 (PDB Primary Data), 3.1.3.99 (UniProt), 2.7.1.77 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49902 (Homo sapiens)
Explore P49902 
Go to UniProtKB:  P49902
PHAROS:  P49902
GTEx:  ENSG00000076685 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49902
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.673α = 90
b = 126.257β = 90
c = 130.706γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
COMOphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA206501
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30CA013696
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10OD012018
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesT32-CA09503

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-07-25
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description