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4Q7Q 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.)

4Q7Q is a homodimeric protein complex that originates from the bacterial species Chitinophaga Pinensis and has a mass of 58.5 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.

1 Overview
- 1.1 General Structure and Origins
- 1.2 Family and Superfamily
2 Structure/Sequence Analysis
- 2.1 Sequence Analysis
- 2.2 Structural Analysis
3 Proposed Functionality

Overview

General Structure and Origins

4Q7Q exists as a homodimer Quaternary structure.^[1] Analyzing primary and Quaternary structures of 4Q7Q with SPRITE and Chimera revealed two chains identical in both shape and sequence^[2] Each chain is 266 residues long, and the entire complex has a molecular weight of approximately 58.5 kDa.^[1].

Primary Sequences of the A and B chains of 4Q7Q.^[2].

4Q7Q proteins primarily appear in bacterial species.^[3]. Research reveals how nearly every enzyme with similar sequencing to 4Q7Q is found in bacterium, with a slight exception to eukaryotes.^[4] 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.^[3].^[5].

Family and Superfamily

Research shows that 4Q7Q is a member of the SGNH Hydrolase protein super family. BLAST and InterPro research suggested 4Q7Q best fits this superfamily, and the known conserved residues seen from SPRITE analysis—Serine, Glycine, Asparagine, and Histidine—line up with those observed throughout this family.^[4]^[6]. Notably, this superfamily is also referred to as the GDSL Hydrolase superfamily.D,E^[4]^[6].

Chimera-generated representation of the A chain of 4Q7Q.^[7]

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.^[8].

Structure/Sequence Analysis

Sequence Analysis

The primary sequence of 4Q7Q shows several conserved sequences between it and esterase-like proteins. A sequence of GDSI—similar to the GDSL sequence seen from its family and superfamily—can be seen between 4Q7Q and enzymes like Isoamyl Acetate-Hydrolyzing Esterase when using DALI.^[9]. Other noteworthy conserved sequences between esterases and 4Q7Q include GxND and DGxH.^[9].

Conserved sequences of note between 4Q7Q and Esterases. ^[9].

These enzymes also share similar secondary structures. Segments of alpha-helixes and beta-sheet strands appear and remain nearly entirely conserved throughout esterase analysis. A few conserved coils appear, but these sections do not appear as often as the other two secondary structures.

Conserved secondary structures of note between 4Q7Q and Esterases. ^[9].

Similar conserved sequences could be found between 4Q7Q and lipases. The GDSI, GxND, and DGxH sequences can be seen from lipases like 7BXD.^[9] The same secondary structure segments can also be located in the lipases analyzed.

Structural Analysis

Right-hand SPRITE analysis revealed 4Q7Q exhibited residues like those seen from enzymes operating with acetyl-like substrates. Specifically, residues Ser. 30, Gly. 69, Asn. 97, Asp. 251, and His. 254 on the A and B chains of 4Q7Q line up with similarly positioned residues on esterases like Platelet-Activating Factor Acetylhyd (PAFA), which exhibited an RMSD of 0.25 angstroms when compared to 4Q7Q.

Other proteins with similar motifs of note are Thioesterase I and Rhamnogalacturonan Acetylesterase, with RMSD values of 0.46 and 0.61, respectively. These alignments focus on the same active site as PAFA did, suggesting the acetyl-like substrates 4Q7Q focuses on are similar to esters.

PFAM graphics from DALI revealed significant structural equivalence between 4Q7Q, a lipase-like protein, Rhamnogalacturonan Acetylesterase, and Sialate O-acetylesterase.

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

Proposed Functionality

Substrates and Docking Analysis

SwissDock analysis showed a preference for larger molecules, specifically fatty acids. Lactide, Ethyl Butyrate, and Triethylene Glycol exhibited noticeably weak binding affinities to the theorized active site of 4Q7Q. These ligands may be ill-suited to act as substrates for 4Q7Q as they are remarkably polar, and lipids—one of the potential categories of substrates for 4Q7Q—are mostly non-polar.

Despite this, these ligands show noticeable hydrophobic interactions with the active site. This implies 4Q7Q uses hydrophobic regions to help guide substrates into the right orientation for enzymatic processes. This also further supports the possibility that 4Q7Q primarily operates with hydrophobic lipid-based substrates. This also explains why Methyl Acetate exhibited a relatively weaker affinity for 4Q7Q, as its smaller structure prevented hydrophobic interactions.

Hypothetical Function

Experimental Data

References

↑ ^1.0 ^1.1 4Q7Q. Protein Database, 2014. https://www.rcsb.org/structure/4Q7Q
↑ ^2.0 ^2.1 Nadzirin, N.; Gardiner, E.; Willett, P.; Artymiuk, P. J.; Firdaus-Raih, M. 2012. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures. Nucleic Acids Res., 40(Web Server Issue), W380-6.
↑ ^3.0 ^3.1 Rio, T. G. D.; et al. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). Stand. Genomic. Sci., 2010, 2(1), 87-95. https://pmc.ncbi.nlm.nih.gov/articles/PMC3035255/
↑ ^4.0 ^4.1 ^4.2 SGNH hydrolase superfamily. InterPro, 2017. https://www.ebi.ac.uk/interpro/entry/InterPro/IPR036514/
↑ Rio, T. G. D.; et al. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). Stand. Genomic. Sci., 2010, 2(1), 87-95. https://pmc.ncbi.nlm.nih.gov/articles/PMC3035255/
↑ ^6.0 ^6.1 Molgaard, A.; Kauppinen, S.; Larsen, S. Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases. Struct., 2000, 8(4), 373-383. https://www.sciencedirect.com/science/article/pii/S0969212600001180?via%3Dihub
↑ UCSF Chimera--a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12.
↑ Akoh, C. C.; Lee, G.; Liaw, Y.; Huang, T.; Shaw, J. GDSL family of serine esterases/lipases. Prog. Lipid Res., 2004, 43(6), 534-552. https://pubmed.ncbi.nlm.nih.gov/15522763/
↑ ^9.0 ^9.1 ^9.2 ^9.3 ^9.4 Holm L, Laiho A, Toronen P, Salgado M (2023) DALI shines a light on remote homologs: one hundred discoveries. Protein Science 23, e4519

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 Research shows that 4Q7Q is a member of the SGNH Hydrolase protein super family. BLAST and InterPro research suggested 4Q7Q best fits this superfamily, and the known conserved residues seen from SPRITE analysis—Serine, Glycine, Asparagine, and Histidine—line up with those observed throughout this family.<ref name="SGNH" /><ref name = "Molgaard">Molgaard, A.; Kauppinen, S.; Larsen, S. Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases. Struct., 2000, 8(4), 373-383. https://www.sciencedirect.com/science/article/pii/S0969212600001180?via%3Dihub</ref>.  Notably, this superfamily is also referred to as the GDSL Hydrolase superfamily.D,E<ref name="SGNH" /><ref name="Molgaard" />.
-[[Image:4Q7QAChain Cartoon Model.png|300px|right|thumb|Chimera-generated representation of the A chain of 4Q7Q.<ref name="Chimera">UCSF Chimera--a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12.</ref>]]
+[[Image:4Q7QAChain.png|300px|right|thumb|Chimera-generated representation of the A chain of 4Q7Q.<ref name="Chimera">UCSF Chimera--a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12.</ref>]]
 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.<ref name="Akoh">Akoh, C. C.; Lee, G.; Liaw, Y.; Huang, T.; Shaw, J. GDSL family of serine esterases/lipases. Prog. Lipid Res., 2004, 43(6), 534-552. https://pubmed.ncbi.nlm.nih.gov/15522763/</ref>.