of PDB Entries for This Enzyme: (RCSB Search Engine)

bioCHEM480 [Autumn 2017]

Inroduction to the Enzyme Bio-informatics project

Edit out any stuff in orange or magenta italics for the final version: Style Counts!
Student Name:

Enzyme Name:

E.C. #: (see #26 at enzyme –database.org)

# of PDB entries for this enzyme: (RCSB search engine)

Authors of paper of PDB data (PDBSum):

Journal Reference:

Pub Med Abstract of paper:

Your Turn:Summary of abstract: (1-3 sentences)
Resolution of X ray data(RSCB or PDBSum):

Source:(various)
Classification/Type of enzyme:(PDBSum):

Reaction:(PDBSum):

Function:(Proteopedia)

Ramachrandran plots(#10)

Number of chains and # of AA in each

Protein Chain(s): # of chains and # of AAs in each chain

Your Turn:summary of what reaction this enzyme catalyses, in which pathway and important structural features (single/multiple sub units, mainly  or secondary structures, etc)

Chain chosen for the analysis below=

ProMotif data:Secondary structure summary (The first table from Promotif documentation)

YourTurn…comment on whether the Rama plot data fits the Promotif secondary structure data.

Wiring Diagram:(from PDBSum stretch to fit width of page)

Domain data:(description) CATHdecdes

Domain images: (shrink to 1-2"x1-2”!)

Ligands:(names and copy and paste image of organic structures):

Metal ions(#14)

Interaction image from ligands (from PDBSum click Ligands tab, LIGPLOT)

Primary sequence in FASTA format:(#16)

FASTA homology data

1. Initial result data(paste in#22 data use the first two sets if the top entry is pretty empty, you both (i) need sequences and (ii) corresponding protein name (i.e on right of sequences))

2. Data by Residue type(#24 data)

Your turn….Deductions from SAS homology data:see (#24 on instructions)

data(see #26-27)

Functional Enzyme Parameters:*Use superscripts correctly in these tables i.e. 10-x….noE-0x

If there’s no data for any of these, put no data

(#28)

Enzyme Class:

Comment:

Reaction Image: C&P

Reaction catalysed by enzyme (Your turn…description in your words)

Pathway: (use 7”x4” image)

Associated disease: Name: (Choose one most related to the pathway you have above)

Your turn….Other searches for associated diseases (OMIM, VVP, Google, Wiki, Proteopedia): a brief overview

RasMol images and analysis (#26…)

Images of overall protein(these three images should be significantly different!)

Images of active site

Images with AA residues and ligands shown

For under each image in legend, list the name and sequence # of each of the AA residues you used and what color each is displayed in: e.g.Gln/Q(122)red

Legend for the 3 images above(i.e. colour coded AA residues and ligands)

Your Turn: The Executive Summary and Analysis

This part is important to the overall score your report will count!

This will include

(1)the role of your enzyme in vivo, i.e reaction, pathway, etc. &

(2)structural features i.e. single/multiple sub units, mainly  or  secondary structures, motifs/domains, etc. &

(3) the role and contents of the active site (especially in light of the AA residues in the active site from the wiring diagram (the green and blue triangles and/or the red/yellow i.e

and the LIGPLOT data from all the other data and your RasMol images.The general idea here is to tie together the information you have (i) collected and (ii) visualized about the active site of your enyme with respect to its biological function (remember Str->Act->Biol Function is the theme of 480)