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Structure of Dipeptidyl peptidase - IV (maybe something like 'Structure')
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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.
Structure
Dipeptidyl peptidase – IV (DPP-IV) is a serine protease, also called adenosine deaminase (ADA) binding protein or CD26. The enzyme is a chain of 766 amino acids and exists in the body as a homodimer. Each monomer of DPP-IV consists of two domains: an 8-bladed β-propeller domain (res. 61-495, shown in green), and an α/β hydrolase domain (res. 39-55 and 497-766, shown in red). The β-propeller domain contains a sequence of stacked β-sheets that form eight propeller-like blades connected to each other via disulfide bonds. [3]
This structure brings rise to a substantial hole in the center of the domain. This domain is important to enzymatic activity as it contains the substrate anchoring residues Glu205 and Glu206. The α/β hydrolase domain contains the catalytic triad of Ser630, His740, and Asp708 (shown in magenta). The triad is essential to substrate binding and hydrolysis at the main active site. The active site of DPP-IV is located at the interface between the two domains. The site has various groups involved in the catalytic process including the previously mentioned catalytic triad and N-terminal anchor, along with the oxyanion hole, hydrophobic pocket, and electrostatic sink.[4]
This interface between the two domains creates a large cavity through the center of the enzyme. This cavity has two openings to the active site: one large hole at the interface between the domains, and the previously mentioned smaller hole located at the center of the β-propeller domain.
Function
DPP-IV is involved in the inactivation of incretins, degradation of non-incretin peptides, and other non-enzymatic functions. Because of this, DPP-IV acts on a wide range of substrates: chemokines (RANTES, MDC, IP-10, etc.), neuropeptides (NPY, Peptide YY, etc.), and regulatory peptides (GLP-1, GLP-2, GIP, etc.). [1] DPP-IV acts on a substrate by hydrolyzing the amide bond at the penultimate residue from its N-terminus, which is either a proline or alanine. [3] For example, the substrate GLP-1 (an incretin important to diabetes research) contains an Ala-His sequence which is cleaved off by DPP-IV. [6]
Research has shown that large substrates like GLP-1 enter DPP-IV through the large cavity formed between its α/β and β domains. After it is cleaved, the large remaining portion of the substrate exits through the same cavity. [3] It is believed that the dipeptide may exit the cavity through the smaller hole formed by the β-propeller region. Antidiabetic drugs called gliptins target and inhibit the DPP-IV enzyme.
Incretins such GLP-1 typically decrease glucose in the blood. When hydrolyzed by DPP-IV, they can no longer defend against high blood glucose. By inhibiting DPP-IV, gliptins increase the number of functional incretins and effectively lower blood glucose.[5]
Relevance
Structural highlights
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References
1. Zhong, J., Rao, X., and Rajagopalan, S. (2013) An emerging role of dipeptidyl peptidase 4 (DPP4) beyond glucose control: potential implications in cardiovascular disease. Atherosclerosis, 226, 305-314. doi: 10.1016/j.atherosclerosis.2012.09.012
2. Hiramatsu, H., Kyono, K., Higashiyama, Y., Fukushima, C., Shima, H., Sugiyama, S., Inaka, K., Yamamoto, A., and Shimizu, R. (2003) The structure and function of human dipeptidyl peptidase IV, possessing a unique eight-bladed -propeller fold. Biochemical and Biophysical Research Communications 302, 849–854. doi:10.1016/s0006-291x(03)00258-4
3. Aertgeerts, K., Ye, S., Tennant, M. G., Kraus, M. L., Rogers, J., Sang, B.-C., Skene, R. J., Webb, D. R. and Prasad, G. S. (2004), Crystal structure of human dipeptidyl peptidase IV in complex with a decapeptide reveals details on substrate specificity and tetrahedral intermediate formation. Protein Science, 13: 412–421. doi:10.1110/ps.03460604
4. Klemann C, Wagner L, Stephan M, von Hörsten S. Cut to the chase: a review of CD26/dipeptidyl peptidase‐4’s (DPP4) entanglement in the immune system. Clinical and Experimental Immunology. 2016;185(1):1-21. doi:10.1111/cei.12781.
5. Dipeptidyl Peptidase-4 (DPP-4). (n.d.). Retrieved January 28, 2018, from https://pdb101.rcsb.org/global-health/diabetes-mellitus/drugs/dpp4-inhibitor/dpp4
6. Chang, X., et al. “Structure and Folding of Glucagon-like Peptide-1-(7-36)-Amide in Trifluoroethanol Studied by NMR.” RCSB PDB, www.rcsb.org/structure/1D0R.
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
- ↑ doi: https://dx.doi.org/10.1016/s0006-291x(03)00258-4
- ↑ doi: https://dx.doi.org/10.1111/cei.12781.
