3QW4

Structure of Leishmania donovani UMP synthase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

The Leishmania donovani UMP synthase is essential for promastigote viability and has an unusual tetrameric structure that exhibits substrate-controlled oligomerization.

French, J.B., Yates, P.A., Soysa, D.R., Boitz, J.M., Carter, N.S., Chang, B., Ullman, B., Ealick, S.E.

(2011) J.Biol.Chem. 286: 20930-20941

  • DOI: 10.1074/jbc.M111.228213
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The final two steps of de novo uridine 5'-monophosphate (UMP) biosynthesis are catalyzed by orotate phosphoribosyltransferase (OPRT) and orotidine 5'-monophosphate decarboxylase (OMPDC). In most prokaryotes and simple eukaryotes these two enzymes are ...

    The final two steps of de novo uridine 5'-monophosphate (UMP) biosynthesis are catalyzed by orotate phosphoribosyltransferase (OPRT) and orotidine 5'-monophosphate decarboxylase (OMPDC). In most prokaryotes and simple eukaryotes these two enzymes are encoded by separate genes, whereas in mammals they are expressed as a bifunctional gene product called UMP synthase (UMPS), with OPRT at the N terminus and OMPDC at the C terminus. Leishmania and some closely related organisms also express a bifunctional enzyme for these two steps, but the domain order is reversed relative to mammalian UMPS. In this work we demonstrate that L. donovani UMPS (LdUMPS) is an essential enzyme in promastigotes and that it is sequestered in the parasite glycosome. We also present the crystal structure of the LdUMPS in complex with its product, UMP. This structure reveals an unusual tetramer with two head to head and two tail to tail interactions, resulting in two dimeric OMPDC and two dimeric OPRT functional domains. In addition, we provide structural and biochemical evidence that oligomerization of LdUMPS is controlled by product binding at the OPRT active site. We propose a model for the assembly of the catalytically relevant LdUMPS tetramer and discuss the implications for the structure of mammalian UMPS.

    Organizational Affiliation: 

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UMP synthase
B, C
453Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BCQ9 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BCQ9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download SDF File 
Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
U5P
Query on U5P
Download SDF File 
Download CCD File 
B, C
URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.236 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 64.722α = 90.00
b = 64.722β = 90.00
c = 477.596γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOLREPphasing
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
ADSCdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-02-29
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description