PDBsum entry 6ddc

Hydrolase

PDB id: 6ddc

Contents

Protein chains

475 a.a.

Ligands

PO4 ×4

Metals

_MG ×2

Waters ×275

PDB id:

6ddc

Name:

Hydrolase

Title:

Crystal structure of the single mutant (d52n) of nt5c2-537x in the basal state, northeast structural genomics consortium target

Structure:

Cytosolic purine 5'-nucleotidase. Chain: a, b. Fragment: residues 1-536. Synonym: cytosolic 5'-nucleotidase ii. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: nt5c2, nt5b, nt5cp, pnt5. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell: rosetta 2(de3).

Resolution:

2.91Å R-factor: 0.187 R-free: 0.264

Authors:

F.Forouhar,C.L.Dieck,G.Tzoneva,Z.Carpenter,A.Ambesi-Impiombato, M.Sanchez-Martin,R.Kirschner-Schwabe,S.Lew,J.Seetharaman, A.A.Ferrando,L.Tong,Northeast Structural Genomics Consortium (Nesg)

Key ref:

C.L.Dieck et al. (2018). Structure and Mechanisms of NT5C2 Mutations Driving Thiopurine Resistance in Relapsed Lymphoblastic Leukemia. Cancer Cell, 34, 136. PubMed id: 29990496

Date:

09-May-18 Release date: 04-Jul-18

Protein chains

P49902  (5NTC_HUMAN) -  Cytosolic purine 5'-nucleotidase from Homo sapiens

Seq: 561 a.a.

Struc: 475 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: E.C.2.7.1.77 - nucleoside phosphotransferase.
• Reaction: a 2'-deoxyribonucleoside + a ribonucleoside 5'-phosphate = a ribonucleoside + a 2'-deoxyribonucleoside 5'-phosphate
• Enzyme class 3: E.C.3.1.3.5 - 5'-nucleotidase.
• Reaction: a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate

ribonucleoside 5'-phosphate + H2O = ribonucleoside + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly)

• Enzyme class 4: E.C.3.1.3.99 - IMP-specific 5'-nucleotidase.
• Reaction: IMP + H2O = inosine + phosphate

IMP + H2O = inosine + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly)

• Cofactor: Divalent metal cation

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Cancer Cell 34:136 (2018)

PubMed id: 29990496

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

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

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.