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3CBW Structure and Proposed Functionality

(NOTE TO ALL EDITORS: This page is part of a final project for a biochemistry lab at Elizabethtown College. Please do not edit this.)

3CBW is a homodimeric protein complex that originates from the bacterial species Chitinophaga Pinensis and has a mass of 80.65 kDa. It is a member of the SGNH Hydrolase Superfamily with structural and sequential similarities to esterases and lipases. Current evidence suggests it causes the hydrolysis of esters and/or acetyl groups on lipids/lipid-like molecules via a serine protease-like active site.

spinqualitylabelsall models 3D Representation of 3CBW Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Overview 3CBW exists as a homodimer quaternary structure.F Analyzing primary and quaternary structures of 3CBW with SPRITE and Chimera revealed two chains identical in both shape and sequence. Each chain is about 300 residues long, and the entire complex has a molecular weight of approximately 80.65 kDa.F 3CBW proteins originate from bacterial species.G,H InterPro search results show how nearly every enzyme with similar sequencing to 4Q7Q is found in various bacteria, with a notable exception to eukaryotes.D Additionally, the PDB entry for 4Q7Q notes how it potentially can be found in Chitinophaga pinensis, a gram-negative bacterial species which can degrade chitin.G,H Family and Superfamily Research shows that 4Q7Q is a member of the SGNH Hydrolase protein super family. BLAST and InterPro both suggested 4Q7Q’s inclusion in this family, and the known conserved residues seen from SPRITE analysis—Serine, Glycine, Asparagine, and Histidine—line up with those observed throughout this family.D,E Notably, this superfamily is also referred to as the GDSL Hydrolase superfamily.D,E 4Q7Q’s inclusion in this family also supports its SPRITE-derived hypothetical functionality. Rhamnogalacturonan Acetylesterase—the enzyme with one of the best SPRITE-based alignment relative to 4Q7Q—is a member of this family.F Proteins in this family are also known for containing a “unique hydrogen bond network that [stabilizes]” the active site.F Regarding what protein family 4Q7Q belongs to, DALI results suggest it is a part of a sub-family of the greater GDSL/SGNH superfamily. A PDB90% DALI search labels 4Q7Q as a part of the “Lipolytic Protein G-D-S-L Family,” which refers to enzymes that hydrolyze lipid substrates. Sequence Analysis (DONE) According to BLAST, 3CBW has similar sequences to 2QHA (Beta-1,4-mannanase) and 2WHK (Mannan endo-1,4-beta-mannosidase). This means that 3CBW is in the mannanase super family. Structural Analysis (DONE) Using Right-hand SPRITE analysis, it showed that 3BCW had similar residues to small amino acid chains. Specific residues are Ala. 76, Ile. 79, Gly. 61, Val. 293, the first two being on the A chain side and the second being on the B chain side of the 3CBW. Comparing 3CBW to 1BHG, which is human beta-glucuronidase, the RMSD value was a difference of 0.46 angstroms. With the use of DALI, it was determined that 3CBW is most similar to Beta-1,4-Mannanase and Mannan Endo-1,4-Beta-Mannosidase. Both of these enzymes hydrolyzes different linkages. Substrates (DONE) Using SwissDock, it was determined that larger, cyclic molecules are good substrates that would have the best binding affinity to 3CBW, each had about a -7 kcal/mol binding affinity. These large molecules are 4-Nitrophenyl N-acetyl-β-D-glucosaminide, 4-Nitrophenyl α-D-glucopyranoside, and p-nitrophenyl phosphate. Theoretical Functionality and Proposed Bodily Purpose According to our research the likely function of this protein is to break down bonds in mannans, glucomannans and galactomannans. The potential substrates and binding sites: 4-Nitrophenyl N-acetyl-β-D-glucosaminide, 4-Nitrophenyl α-D-glucopyranoside, and P-Nitrophenyl Phosphate

References (DONE)

A) Dhawan, S.; Kaur, J.; Microbial Mannanases: An Overview of Production and Applications. Critical Reviews in Biotechnology 2007, 27, 197-216. DOI: 10.1080/07388550701775919 B) Soni, H.; Rawat, H. K.; Pletschke, B. I.; Kango, N. Purification and characterization of Beta-mannanase from Aspergillus terreus and its applicability in depolymerization of mannans and saccharification of lignocellulosic biomass. Biotech 2016, 6, 136. DOI: 10.1007/s13205-016-0454-2 C) Cheng, L.; Duan, S.; Feng, X.; Zheng, K.; Yang, Q.; Liu, Z. Purification and Characterization of a Thermostable Beta-Mannanase from Bacillus subtilis BE-91: Potential Application in Inflammatory Diseases. BioMed Research International 2016, 2016, 1-7. DOI: 10.1155/2016/6380147

Proteopedia Page Contributors and Editors (what is this?)

Sophia Calzola, Angelina Giglio-Tos