Explore Enzyme Portal

Hi I’m Jenny Cham and I work at the European Bioinformatics Institute in Cambridge, UK. I’m going to show you an example of how you might use EBI’s Enzyme Portal. Why you might you want to use the Enzyme Portal? You might have heard about an interesting enzyme and want to find out more about it. Or perhaps you are doing research into a particular disease, and want to see whether proteins with enzymatic activity are involved - and if there are drug compounds to target it. Enzyme portal offers a comprehensive summary of this kind of information. So let’s have a go! I’m going to look up phenylalanine hydroxylase.I typed in the name but if I had a specific family member in mind, I could also use the UniProtKB ID or PDBe code - enzyme classification numbers also work. In the results page, if you get lots of results like this, you can refine your search using the facets on the left. I just want to look at entries with information for human, so I’ll check the box here. The filter is dynamic, so when I select the filter it automatically updates the results list. Each box in the hit list represents a specific enzyme. It shows me its primary name, any other names and functional information if available. You can also see the species for which enzyme-related information has been found. The ribbon structure icons show you straightaway whether there is a 3D protein structure available for the enzyme. This one is in colour because there is a structure in PDBe - if it hasn’t been elucidated yet then it appears in grey. Like this one. OK so I’m going to now look at phenylalanine-4- hydroxylase. Immediately I come to an interactive summary report. What’s nice about this is that it orders the information according to different areas of biology and chemistry. I’ll take you through each of these tabs. The enzyme tab gives an overview of function. It also has the classification of the type of reactions catalysed by the enzyme. There is a quick link directly to the protein’s amino acid sequence. The source of the information is at the bottom of the tab. In this case the information comes from IntEnz and UniProtKB databases. In the next tab we can see the 3D ribbon structure from the protein databank (PDBe). When you click on the image it takes you to a viewer where you can manipulate the structure. For example you can switch off and on the surface. The green menu at the top shows all the structures available for the enzyme, there may be several for well characterised proteins. The next tab includes the reaction with chemical structures at the top and the pathways in which the reaction is found below. This example does not have a pathway, but you can see in this other example here, for cytochrome P450, what it looks like when there are pathway informations available. Here for example: biological oxidation with text and graphics and also a catalyic cycle here. In the Small molecules tab you can explore drug-like compounds that may interact with the enzyme. Disease information for the enzyme is taken from UniProt and includes information that references OMIM. In Literature you can find papers related to this enzyme. You can switch to view the papers just relating to the enzyme itself or to its 3D structure information. To read the abstract just click on ‘Toggle abstract’. In all of the tabs, you will find links that take you directly to the source information for the fact presented. For example, in enzyme tab it says that this protein has 452 amino acids, so if you want to see the sequence for yourself you click on the link and it takes you directly to UniProt in the correct place in the record. You can also use the species selector at the top to explore other species of interest, such as model organisms of disease. For example, if I switch to C. elegans you can see the protein sequence changes. Now you see the protein sequence has changed to 457 amino acids. Once you are ready to search again, just go back to the results page or the Enzyme Portal homepage, using the breadcrumbs. So give it a go, and let us know what you think!