A phylogenetic study of ubiquitin conjugating enzymes and structural analysis of human UBE2J proteins

The ubiquitin proteasome system (UPS) is responsible for the degradation and turnover of proteins in eukaryotes. As such it is a key process that is involved in normal and in some cases, abnormal cellular functions. Ubiquitin conjugating enzymes (UBCs) are key components of the UPS and may serve as therapeutic targets.<br/><br/>The aims of this project are the structural and functional analyses of UBCs in eukaryotic organisms whose genomes have been fully sequenced, and also the review of the nomenclature of yeast and human UBCs. The main findings were:<br/><br/>1) The successful construction of Phylogenetic trees containing all 14 yeast UBCs and UBC-like proteins and their homologues in selected species whose genomes have been fully sequenced. The phylogenetic tree consists of 15 different branches. Thirteen of the branches contain a member of the yeast UBC or UBC-like family (MMS2) and their homologues. The remaining two branches contain firstly the human UBE2L proteins and secondly the TSG101 UBC like proteins, both of which branches do not appear to have any yeast orthologues.<br/><br/>2) The UBC phylogenetic study was also used to identify the previously unknown UBC active site of the <i>Drosophila </i>transcription factor, TAF_II250. Using multiple sequence manual alignments of known TAF_II250 and UBC protein sequences a putative UBC active site in <i>Drosophila melanosaster</i> and <i>Apis mellifera</i> TAF_II250 was successfully identified, and was shown to share approximately 70% homology to the known UBC PROSITE signature.<br/><br/>3) Using multiple sequence alignments the hitherto unknown PROSITE signature of the clinically important UBE2J family was identified. This PROSITE signature is very different from all other UBCs suggesting that this family of enzymes has significant structural changes at their active sites. Homology modelling proved to be a successful approach to obtain structural information of the UBE2J1 active site. Superimposition studies using the previously solved structures for human UBE2J2 and human UBC9 were carried out. Significant differences were observed near the active sites of human UBE2J proteins compared to the active site for human UBC9.

Name dc:type.qualificationname

PhD

Level dc:type.qualificationlevel

Doctoral Thesis

Grantor dc:publisher.institution

University of Abertay Dundee

Year dc:date.issued

2006

Author dc:creator

• Mukherjee, Joy

Advisor dc:contributor.advisor

• Lester, Douglas

Language dc:language

eng

Identifier

oai:rke.abertay.ac.uk:studenttheses/3908152f-5fa6-4fce-98bd-e316d5fd046d

OAI identifier oai:identifier

oai:rke.abertay.ac.uk:studenttheses/3908152f-5fa6-4fce-98bd-e316d5fd046d