6DDZ

Crystal structure of the double mutant (D52N/R238W) of NT5C2-537X in the active state, Northeast Structural Genomics Target


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytosolic purine 5'-nucleotidase554Homo sapiensMutation(s): 2 
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
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.677α = 90
b = 127.293β = 90
c = 131.131γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
COMOphasing

Structure Validation

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Ligand Structure Quality Assessment 


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, Derived calculations, Refinement description