PDBsum entry 3euf

Transferase

PDB id: 3euf

Contents

Protein chain

293 a.a. *

Ligands

BAU ×4

PO4 ×4

Waters ×336

* Residue conservation analysis

PDB id:

3euf

Name:

Transferase

Title:

Crystal structure of bau-bound human uridine phosphorylase 1

Structure:

Uridine phosphorylase 1. Chain: a, b, c, d. Synonym: urdpase 1, upase 1. Engineered: yes

Source:

Homo sapiens. Organism_taxid: 9606. Gene: upp1, up. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.205 R-free: 0.251

Authors:

T.P.Roosild

Key ref:

T.P.Roosild et al. (2009). Implications of the structure of human uridine phosphorylase 1 on the development of novel inhibitors for improving the therapeutic window of fluoropyrimidine chemotherapy. Bmc Struct Biol, 9, 14. PubMed id: 19291308

Date:

10-Oct-08 Release date: 31-Mar-09

Protein chains

Q16831  (UPP1_HUMAN) -  Uridine phosphorylase 1 from Homo sapiens

Seq: 310 a.a.

Struc: 293 a.a.

Enzyme reactions

• Enzyme class: E.C.2.4.2.3 - uridine phosphorylase.
• Reaction: uridine + phosphate = alpha-D-ribose 1-phosphate + uracil

uridine (Bound ligand (Het Group name = PO4) corresponds exactly) + phosphate (Bound ligand (Het Group name = BAU) matches with 60.87% similarity) = alpha-D-ribose 1-phosphate + uracil

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

reference

Bmc Struct Biol 9:14 (2009)

PubMed id: 19291308

Implications of the structure of human uridine phosphorylase 1 on the development of novel inhibitors for improving the therapeutic window of fluoropyrimidine chemotherapy.

T.P.Roosild, S.Castronovo, M.Fabbiani, G.Pizzorno.

ABSTRACT

BACKGROUND: Uridine phosphorylase (UPP) is a key enzyme of pyrimidine salvage pathways, catalyzing the reversible phosphorolysis of ribosides of uracil to nucleobases and ribose 1-phosphate. It is also a critical enzyme in the activation of pyrimidine-based chemotherapeutic compounds such a 5-fluorouracil (5-FU) and its prodrug capecitabine. Additionally, an elevated level of this enzyme in certain tumours is believed to contribute to the selectivity of such drugs. However, the clinical effectiveness of these fluoropyrimidine antimetabolites is hampered by their toxicity to normal tissue. In response to this limitation, specific inhibitors of UPP, such as 5-benzylacyclouridine (BAU), have been developed and investigated for their ability to modulate the cytotoxic side effects of 5-FU and its derivatives, so as to increase the therapeutic index of these agents. RESULTS: In this report we present the high resolution structures of human uridine phosphorylase 1 (hUPP1) in ligand-free and BAU-inhibited conformations. The structures confirm the unexpected solution observation that the human enzyme is dimeric in contrast to the hexameric assembly present in microbial UPPs. They also reveal in detail the mechanism by which BAU engages the active site of the protein and subsequently disables the enzyme by locking the protein in a closed conformation. The observed inter-domain motion of the dimeric human enzyme is much greater than that seen in previous UPP structures and may result from the simpler oligomeric organization. CONCLUSION: The structural details underlying hUPP1's active site and additional surfaces beyond these catalytic residues, which coordinate binding of BAU and other acyclouridine analogues, suggest avenues for future design of more potent inhibitors of this enzyme. Notably, the loop forming the back wall of the substrate binding pocket is conformationally different and substantially less flexible in hUPP1 than in previously studied microbial homologues. These distinctions can be utilized to discover novel inhibitory compounds specifically optimized for efficacy against the human enzyme as a step toward the development of more effective chemotherapeutic regimens that can selectively protect normal tissues with inherently lower UPP activity.