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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Proteopedia Final Assignment

• • • IMAGES***

1c) 3a) . 3c) . 4a) 4b) 4c) . 5a) ii) iii)

• • • PRESENTATION INFORMATION***

Discussed the function of your protein and utilized images on the page to explain that function

i. The organism the protein is from is Bacillus cereus which is a gram-positive, rod bacterium.

ii. The basic job of UGA epimerase (UGAepi) is to turn UDP-Glucuronic Acid into UDP-Galacturonic Acid. Essentially, it turns glucose into a galactose molecule by flipping one of the chiral centers. The name of the enzyme is also intuitive because glucose and galactose are epimers of each other in that only one chiral center are different. This enzyme is different than the others outlined because it does not do decarboxylation.

iii. file:///C:/Users/17longm17/Downloads/UGAepi.pdf

Discussed biological relevance and broader implications

i. UGAepi turns glucose into a galactose without undergoing decarboxylation. The “swing and flip” rotation appears to be unique or abnormal. The “swing and flip” rotation outlines a change from UDP-glucuronic acid (substrate) to UDP-galacturonic acid (product). The molecules, whether the substrate or the product, appear to be reacting with or under the presence of NAD+ and Tyr149.

ii. file:///C:/Users/17longm17/OneDrive/Documents/swing%20and%20flip.pdf

iii. Studying this organism is very relevant. The epimerase inverts the stereochemistry of UDP-sugar carbons that have been investigated. Epimerization by UDP-galactose 4-epimerase has been studied and found to be a part of the Leloir pathway. The pathway converts UDP-glucose to UDP-galactose and vice versa. It also belongs to the SDR family. Because of the intense amount of research and findings, this organism is very relevant now.

Discussed important amino acids and utilized images on the page to support the discussion

i.Ligands are UGA and UGB (look at three ligand images)

ii. Important amino acids are:

1. 1. ARG 192- basic interaction 2. 2. SER 272- hydrophilic interaction 3. 3. ASP 187- acidic interaction 4. 4. TYR 176-hydrophobic interaction 5. The four amino acids listed above are capable of participating in the catalytic process as proton donors or proton acceptors. Amino acids that are important for the ligand binding have acid-base catalysis properties

iii. Catalytic Triad- “Ser/Thr-Tyr-Lys.” (look at catalytic triad image)

Discussed structural highlights and utilized images on the page to explain those highlights

i. Active site- There is an active site at the C-terminus that is for binding.

ii. Quarternary Structure- (show quarternary structure figure as well as secondary structure figure)

         a. It is evident that there is a quaternary structure because there are two polypeptides. Along those same lines, it is a homodimer with a strong hydrophobic 
           interaction base. 
         b. Cleft for substrate binding was also identified within the protein and showcased in an image (show cleft figure)

iii. Rossmann Fold-

         a. file:///C:/Users/17longm17/Downloads/Rossman%20Fold.pdf

1. Rossman folds are critical to the function of the protein. 2. As defined in Proteopedia, “The Rossmann fold is a super-secondary structure that is characterized by an alternating motif of beta-strand-alpha helix-beta strand secondary

  structures.”

3.The Rossmann fold is within the N-terminal domain.

Discussed other important features and utilized images on the page to explain those features

i. Motif- smaller structural element repeated in proteins (5-10 amino acids)

               “Tyr-X-X-X-Lys motif of the Ser/Thr-TyrLys triad, the typical hallmark of SDR enzyme”
       	***X means any other amino acids

ii. Intermolecular Forces- 1. Hydrogen Bonding (show hydrogen bond figure)- many hydrogen bonds are found in the protein 2. Pi Stacking- Pi stacking is present, but less commonly found when compared to hydrogen bonds 3. Hydrophobic Interactions (show hydrophobic interaction figure)-Because the protein had a quarternary structure, there is a hydrophobic core between the two polypeptides.

iii. Structure and Function relationship- “The N-terminal domain is characterized by a Rossmann fold motif comprising a core of seven b-strands surrounded by six a-helices. The NAD1 cofactor is fully embedded within this domain, whereas the smaller C-terminal domain provides the binding site for the UDP-GlcA substrate. The crevice between the two domains encloses the active site.” (show N and C terminus image)

• • • Much more information to be found on the attached word document***

REFERENCES FOR OUTSIDE IMAGES

1. UGAepi- Figure- Scheme 1

2. swing and flip- Supporting Information Section

3. Rossman fold- Figure 1

SOURCE:

Iacovino, Luca Giacinto et al. “Crystallographic snapshots of UDP-glucuronic acid 4-epimerase ligand binding, rotation, and reduction.” The Journal of biological chemistry vol. 295,35 (2020): 12461-12473. doi:10.1074/jbc.RA120.014692