Sandbox 179
From Proteopedia
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==Historical Facts== | ==Historical Facts== | ||
| - | Theodor Schwann discovered [http://en.wikipedia.org/wiki/Pepsin pepsin] in 1836. He named the enzyme pepsis from the Greek word peptein which means to digest. | + | Theodor Schwann discovered [http://en.wikipedia.org/wiki/Pepsin pepsin] in 1836. He named the enzyme pepsis from the Greek word peptein which means to digest. Pepsin was the first animal enzyme to be discovered, and, in 1929, it became one of the first enzymes to be crystallized, by John H. Northrop. |
| + | They were also the first protein crystals to be studied by X-ray diffraction using the method of capillary mounting to prevent water loss <ref name="Xray">PMID: 2115088</ref>. | ||
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==Protein Function== | ==Protein Function== | ||
Revision as of 03:50, 31 March 2010
| Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. Andrea Gorrell. | |||||||||
Contents |
Pepsin
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| 5pep, resolution 2.34Å () | |||||||||
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| Activity: | Pepsin A, with EC number 3.4.23.1 | ||||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Historical Facts
Theodor Schwann discovered pepsin in 1836. He named the enzyme pepsis from the Greek word peptein which means to digest. Pepsin was the first animal enzyme to be discovered, and, in 1929, it became one of the first enzymes to be crystallized, by John H. Northrop. They were also the first protein crystals to be studied by X-ray diffraction using the method of capillary mounting to prevent water loss [1].
Protein Function
Pepsin is one of three proteolytic, or protein degrading enzymes in the digestive system. It resides in the alimentary canal and is produced by mucosal cells. Pepsin degrades peptides, and is optimally active at low pHs [1]. Pepsin is an aspartic proteinase, more specifically a eukaryotic aspartic protease enzyme. Pepsin was among the first enzymes to be isolated in crystalline form [2]. Aspartic proteinases are widespread in nature, and pepsin in particular has been known to be medically important [3].
Overall Structure
Pepsin is bilobal, composed of two nearly equal N and C domains related by an intra dyad [2]. Each of these domains consists predominantly of β-sheets [2]. 44% of the structures residues are within a β-sheet, although there are six small right-handed α-helical segments, the longest being hc which spans from residues 225-236. All of the a-helices except h'c are partially exposed and have some amphiphilic character especially hc, which has a solvated surface and a buried side [1]. The two most prominent strands of mixed β-sheets are 1N and 1C, these sheets are related by an intra-lobe topological 2-fold symmetry. The most important β-sheet consists of six anti-parallel β-strands. “Two further β-sheets, 2N and 2C are each related by an intra-lobe topologically related β-hairpins, folded below the 1N and 1C sheets. further, a six-stranded sheet spans the two lobes and forms a structure resembling an arch upon which the other four strands reside [1].” The interface between sheets 1N and 1C forms the catalytic center consisting of the nearly co-planar carboxyl group of aspartate residues , which are held in close proximity by a network of hydrogen bonds, and which are shielded from solvents by a β-hairpin loop. Both catalytic residues may be protonated, although only one carboxyl group would be negatively charged at any one time [1]. The overall peptide folds and active sites structures are homologous [2]. Aspartic proteinases, including pepsin are distinguishable by the presence of two conserved aspartic acid residues in the active site [2]. Each domain in pepsin contains one of two catalytically important aspartic acid residues [2]. There are 326 residues in pepsin, forming two topologically similar lobes. Residues 1-175 form the N-terminal lobe, and residues 176-327 constitute the C-terminal lobe. A large portion of the residues are polar and buried [1]. The side chains are involved in hydrogen-bond interactions with the main chain of the protein or other conserved side-chains of the enzyme [1].” Hydrogen-bonds are what stabilize the fold of pepsin, this stabilizing is called the fireman`s grip. About 188 main-chain-main –chain hydrogen bonds exist. The enzyme also has a high proportion of serine and threonine residues, the total being 60. Of these, 32 are involved with side-chain hydrogen-bond interactions with other residues of the enzyme. There are 2425 non-hydrogen protein atoms and 371 water molecules [1] . Pepsin has a very low pI in the range of 2-3 pH units, which is due to the high proportion of carboxyl residues, 43. The protein is phosphorylated at Ser68 and has three disulphide bridges. Pepsin also contains several salt-bridges one of which from 206 to 210 encloses the pepsins only type II turn. Type I turns are the most prevalent in pepsin [1]. There are typically three basic residues in pepsin, Arg308, His53, and Lys320.
What are the Structures Implications?
One of the main salt bridges in pepsin includes residues from one of the dyad-related hylices (h’N and h’C) and a residue from the opposite lobe, e.g. Asp138 interacts with Arg316. This ion-pair may be important for the stability of the pepsin fold, since chemical modification of Arg316 with butane-2,3-dione partially inactivates the enzyme, as does treatment with phenylglyoxal [1]. There are many sub domains in pepsin. One sub domain which includes the residues 222-235; 255-276; and 283-290. Portions of this sub domains can interact with inhibitors, and therefore contribute to the structural delineation of S’ sub sites [2]. It is also possible that ridged movements of sub domains relative to the large domain may help the enzyme adjust to various substrate structures. Furthermore, local regional flexibility of structures such as the “flap,” in and around the active site of pepsin has been suggested to modulate substrate and inhibitor binding [2].
Once denatured, pepsin is unable to refold to an active native state upon returning from denaturing conditions. One proposed solution for this is that pepsin formation depends on a separate prosegment (PS) domain. When returning from the denatured state, the denatured pepsin first has to bypass a large folding barrier and then in the presence of PS the native state can become thermodynamically stable. The PS therefore can catalyze pepsin folding by stabilizing the transition state [3] .
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Cooper JB, Khan G, Taylor G, Tickle IJ, Blundell TL. X-ray analyses of aspartic proteinases. II. Three-dimensional structure of the hexagonal crystal form of porcine pepsin at 2.3 A resolution. J Mol Biol. 1990 Jul 5;214(1):199-222. PMID:2115088
- ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 Abad-Zapatero C, Rydel TJ, Erickson J. Revised 2.3 A structure of porcine pepsin: evidence for a flexible subdomain. Proteins. 1990;8(1):62-81. PMID:2217165 doi:http://dx.doi.org/10.1002/prot.340080109
- ↑ 3.0 3.1 The prosegment catalyzed pepsin folding to a kinetically trapped native state. Biochemistry 49:365-371
