Sandbox Reserved 315

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This Sandbox is Reserved from January 10, 2010, through April 10, 2011 for use in BCMB 307-Proteins course taught by Andrea Gorrell at the University of Northern British Columbia, Prince George, BC, Canada.
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Introduction

Orotidine monophosphate decarboxylase (ODCase), also known as orotidine 5’-monophosphate decarboxylase (OMP decarboxylase) or orotidine 5’-phosphate decarboxylase is an enzyme involved in pyrimidine biosynthesis. It catalyzes the conversion of orotidine 5’-monophosphate (OMP) to uridine 5’-monophosphate (UMP). This reaction is the final step in de novo pyrimidine nucleotide synthesis and is an essential precursor for both DNA and RNA. The main structure of orotidine monophosphate decarboxylase is a TIM barrel, with one side acting as the binding site, while the other side is closed-off. This enzyme has been studied for it’s extreme catalytic proficiency[1].

Contents


PDB ID 1dv7

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1dv7, resolution 1.80Å ()
Activity: Orotidine-5'-phosphate decarboxylase, with EC number 4.1.1.23
Related: 1dvj
Resources: FirstGlance, OCA, RCSB, PDBsum, TOPSAN
Coordinates: save as pdb, mmCIF, xml


Structure

TIM Barrel

Active Site

  • first bullet
    • sub-bullet
  • second bullet[2]
    • α
  1. category 1 [2]
    1. 2

Wikipedia

Function

Insert caption here

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UMP Synthase

In multicellular eukaryotes, orotidine monophosphate decarboxylase associates with orotate phosphoribosyltransferase to form a bifunctional protein, UMP synthase[3][4]. UMP synthase carries out the last two steps in pyrimidine biosynthesis, converting orotate to uridine 5'-monophosphate[4]. This reaction involves first adding ribose-P to orotate to form orotidine 5'-monophosphate, followed by a decarboxylation reaction to form uridine 5'-monophosphate[4]. In microorganisms these two enzymes are separate and coded by distinct genes. However research has shown that all multicellular eukaryotes so far code the genes for these two enzymes together and as a result they are covalently bonded as a bifunctional protein with two distinct catalytic domains[4].

Rate of Catalysis

Substrate Destabilization

[3]

References

  1. ↑ Miller BG, Hassell AM, Wolfenden R, Milburn MV, Short SA. Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog. Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2011-6. PMID:10681417 doi:10.1073/pnas.030409797
  2. ↑ 2.0 2.1 Wu N, Mo Y, Gao J, Pai EF. Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase. Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2017-22. PMID:10681441 doi:10.1073/pnas.050417797
  3. ↑ 3.0 3.1 Lee JK, Houk KN. A proficient enzyme revisited: the predicted mechanism for orotidine monophosphate decarboxylase. Science. 1997 May 9;276(5314):942-5. PMID:9139656
  4. ↑ 4.0 4.1 4.2 4.3 Yablonski MJ, Pasek DA, Han BD, Jones ME, Traut TW. Intrinsic activity and stability of bifunctional human UMP synthase and its two separate catalytic domains, orotate phosphoribosyltransferase and orotidine-5'-phosphate decarboxylase. J Biol Chem. 1996 May 3;271(18):10704-8. PMID:8631878
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