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UCHL3 in Plasmodium falciparum

Morgan Korinek '12 and Andrea Pohly '12


Contents:

I. Introduction

II. General Structure

III. Crossover Loop

IV. Differences between HsUCHL3 and FsUCHL3

V. Dual Ubiquitin and Nedd8 Specificity

VI. References


I. Introduction

Malaria is one of the most-widespread infectious diseases affecting people around the globe.  Malaria is caused by protists of the genus Plasmodium and is transmitted through the blood by mosquitoes.  The replication of Plasmodium parasites in red blood cells can cause a human host to develop symptoms such as a headache and/or fever, but can also can have more severe consequences such as a coma or even death.  While there are 5 different species of Plasmodium, the most severe form of malaria is caused by one species in particular: Plasmodium falciparum.  

PfUCHL3, a ubiquitin C-terminal hydrolase (UCH),  is thought to be essential for Plasmodium falciparum to survive.  Ubiquitin (Ub) is a protein present in all eukaryotes that is composed of a well-conserved sequence of 76 amino acids. This ubiquitin-proteosome system is crucial to eukaryotic survival and is involved in protein degradation as well as cell's maintenance of synthesized and degraded proteins.  When this balance is out of equilibrium, the cell can run into functional problems and can eventually lead to cell death.  (3)

In this tutorial, we examine the structure of pfUCHL3 and how it differs from Hs, or human, UCHL3.  Because pfUCHL3 binds ubiquitin differently than its human counterpart, this protein is a potential drug target for malarial patients.  


II. General Structure

 PfUCHL3 consists of a central six-stranded anti-parallel β-sheet surrounded by seven α-helices  Viewing PfUCHL3 in complex with a ubiquitin-based suicide substrate (UbVME) allows us to show the dual specificity of this enzyme. . The β –sheet conformation of the C-terminus of Ubiquitin has backbone carbonyl and amide groups that  hydrogen bonds to the PfUCHL3 residues.  The C-terminus of Ubiquitin binds to the narrow groove, lined by the catalytic triad residues: Cys-92, His-164, and Asp-179  These three residues are all within hydrogen bonding distance of each other. .   Ser-12 forms an additional hydrogen bond to the backbone nitrogen of Ub Leu-73 in the Ub-binding groove of PfUCHL3.    All of the hydrogen bond donors and acceptors of Ub C-terminal residues 71-75 are then fulfilled. (1)

III. Crossover Loop

An important element of the bound complex is the active site crossover loop.  In unbound PfUCHL3, the crossover loop is very ordered.  This is due to crystal contacts that hold the loop in a distinct conformation.  No significant structural changes occur upon the binding of Ubiquitin.  (5)

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825479/figure/F4/

This loop encounters the C-terminal of the Ubiquitin suicide substrate (UbVME) and is thought to assist in the positioning of the substrate.  When the substrate is not present, the crossover loop becomes flexible and cannot be detected in the crystal structure, hence why we cannot see it on this free molecule.  However, when ubiquitin is present, the crossover loop connects the two halves of the catalytic center, bringing key residues close enough to catalyze the binding of ubiquitin.  The crossover loop also functions as a substrate filter by limiting the types and sizes of substrates the enzyme can hydrolyze.  While the structure and function of the cross-over loop is not yet well understood, there are a few key features that are visible in the ubiquitin bound crystal structure.   Leu-71 and Leu-73 point to the opposite side of the binding groove and occupy a hydrophobic binding pocket where the substrate attaches. Asp- 157 is located in the crossover loop and forms a salt bridge with the side chain of Arg-74 of Ub to provide stability to the bound complex. This ubiquitin binding pocket can now be visualized. (1)


IV. Differences between HsUCHL3 and FsUCHL3

The key difference between HSUCHL3 and FsUCHL3 is that the sequence of the crossover loop is not conserved.  Therefore, these two enzymes do not interact with Ub in the same pattern and do not share the same conformation.  While the Ub recognition and binding mode between each enzyme and Ub is similar, the Ub interface of both enzymes have a few key differences.  In PfUCHL3, Ser-12 in the Ub-binding-groove forms an additional hydrogen bond to the backbone nitrogen of Ub Leu-73.  Ub-Arg-74, a highly conserved residue and central to Ub recognition, forms a network of hydrogen bonds with HsUCHL3 residues.  However, PfUCHL3 residues have a completely different  conformation of hydrogen bonds.  One example of this is the formation of a salt bridge to Asp-157 in PfUCHL3 that is not present in HsUCHL3.  Also, the interface of PfUCHL3 and Ub have the nonconserved residues of Thr-163 and Ser-219 .  These key differences allow researchers to specifically target the parasite rather than the human host cells. (1)

V. Dual Ubiquitin and Nedd8 Specificity

PfUCHL3 is the only deNeddylase present in the parasite's genome.  The Nedd8 protein is involved in the control of the G1 to S phase of the cell cycle.  Interferring with the Nedd8 pathway can cause the cells to bridge multiple S phases and fail to undergo mitosis.  By interferring with the enzyme that processes Nedd8, researchers can disrupt the cell cycle and ultimately lower the cell's viability.  (1)

An interesting feature of UCHL3 is that it can bind both Ubiquitin as well as Nedd8.  Arg-72 in Ubiquitin, which corresponds to Gln-72 of PfNedd8, readily hydrogen bonds to Glu-11 and Asn-13 of PfUCHL3.  These interactions suggest that both Ubiquitin and PfNedd8 are natural substrates of PfUCHL3.  Further research is still in progress in determining if Nedd8 could be a possible drug target for malaria as well.  (2)


VI. References

(1) Artavanis-Tsakonas, K., W.A. Weihofen, J.M. Antos, B.I. Coleman, C.A. Comeaux, M.T. Duraisingh, R. Gaudet and H.L. Ploegh. 2010. Characterization and Structural Studies of the Plasmodium falciparum Ubiquitin and Nedd8 Hydrolase UCHL3.  The Journal of Biological Chemistry 285(9): 6857-6866.

(2) Artavanis-Tsakonas, K., S. Misaghi, C.A. Comeaux, A. Catic, E. Spooner, M.T. Duraisingh and H.L. Ploegh. 2006. Identification by functional proteomics of a deubiquitinating/deNeddylating enzyme in Plasmodium falciparum.  Molecular Microbiology 61(5): 1187-1195.

(3) Kim, J.H., K.C. Park, S.S. Chung, O. Bang and C.H. Chung. 2003. Deubiquitinating Enzymes as Cellular Regulators.  J. Biochem 134(1): 9-18.

(4) Pickart, C.M. and M.J. Eddins. 2004. Ubiquitin: structures, functions, mechanisms. Biochimica et Biophysica Acta 1695: 55-72.

(5) Popp, M.W., K. Artavanis-Tsakonas and H.L. Ploegh. 2009. Substrate Filtering by the Active Site Crossover Loop in UCHL3 Revealed by Sortagging and Gain-of-function Mutations. The Journal of Biological Chemistry 284(6): 3593-3602.

(6) Wilkinson, K.D. 1997. Regulation of ubiquitin-dependent processes by deubiquitinating enzymes. The FASEB Journal  11(1): 1245-1256.

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