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Human HMG-CoA Reductase Catalytic Domain, 1dqa

PDB ID 1dq8 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
Crystal Structure of Human HMG-CoA Reductase Catalytic Domain, 1dq8
Ligands:	, ,
Activity:	Hydroxymethylglutaryl-CoA reductase (NADPH), with EC number 1.1.1.34
Structural annotation: Resources: CATH : 1Dq8A03, 1Dq8A02, 1Dq8A01, 1Dq8B02, 1Dq8B01, 1Dq8B03, 1Dq8C02, 1Dq8C01, 1Dq8C03, 1Dq8D03, 1Dq8D02, 1Dq8D01 InterPro : Ipr009023, Ipr000731, Ipr002202, Ipr004816, Ipr004554, Ipr009029 Pfam : PF00368 SCOP : d1dq8a4, d1dq8a1, d1dq8b4, d1dq8b1, d1dq8c1, d1dq8c4, d1dq8d1, d1dq8d4 UniProt : P04035
Functional annotation: Cellular component: membrane fraction endoplasmic reticulum endoplasmic reticulum membrane membrane peroxisome integral to membrane Biological process: germ cell migration lipid metabolic process cholesterol biosynthetic process gonad development sterol biosynthetic process cholesterol metabolic process lipid biosynthetic process biosynthetic process steroid biosynthetic process Molecular function: oxidoreductase activity hydroxymethylglutaryl-CoA reductase (NADPH) activity
Evolutionary conservation: Toggle Conservation Colors: Rows = identical sequences: Further Information: Caveats, Explanation, Complete Results at ConSurfDB
Resources:	FirstGlance, OCA, RCSB, PDBsum
Coordinates:	save as pdb, mmCIF, xml

HMG-CoA Reductase (or 3-hydroxy-3-methyl-glutaryl-CoA reductasese or HMGR) is the rate-controlling enzyme of the mevalonate pathway, responsible for cholesterol and other isoprenoid biosynthesis. HMGR is a polytopic, transmembrane protein, containing 8 domains, that is anchored in the membrane of the endoplasmic reticulum.^[1] It is the major target of the Statins, a cholesterol lowering drug class and the best selling pharmaceutical drugs in the world.

Mevalonate Pathway. Note the early stage at which the statins interfere in the pathway

Biological Role

HMGR is among the most highly regulated enzymes in the human body. It catalyzes the formation of mevalonic acid, the committed step in the biosynthesis of sterols, most notably cholesterol. This reaction can be seen below where HMG-CoA is reduced by NADPH. Despite the poor reputation cholesterol has in the media, it is a critical component of cellular membranes as it is required to establish proper membrane permeability and fluidity. The mevalonate pathway is also responsible for synthesis of the oxygen transporting heme found in red blood cells. ^[2]

Structure

Structure of HMG-CoA reductase (PDB entry 1dq8) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image General Structure There are two distinct classes of HMGRs, class I, which is only found in eukaryotes and are membrane bound and class II, which is found in prokaryotes and are soluble. [3] HMGR contains 8 transmembrane domains that have yet to be successfully crystallized, which anchor the protein to the membrane of the endoplasmic reticulum. [1] The catalytic portion of human HMGR forms a tetramer, with the individual monomers winding around each other. [1] Within the tetramer, the monomers are arranged into , each of which contains which are formed by residues form both monomers. Each monomer contains , the , the , and the . The L-domain is unique to HMGRs while the S-domain, which forms the binding site for NADP, resembles that of ferredoxin. The S and L domains are connected by a which is essential for the HMG-binding site. [1] Salt bridges between residues R641 and E782 as well as between E700 and E700 on neighboring monomers compliment the largely hydrophobic dimer-dimer interface.[1] Substrate Binding & Catalytic Mechanism Chemical Reaction Catalyzed by HMGR The HMG-CoA and NADPH molecules make numerous contacts with the in forming the four active sites. The CoA is located in a , with the pantothenic acid moiety extending into the interior of the protein. over the CoA adenine base, shielding the extended binding pocket from solution. The NADPH binding site is formed primarily by the S-domain with playing a critical role in binding.[1] The HMG binding pocket is the site of catalysis in HMGR. is a critical structural element of this binding site. Residues and are positioned in the active site as is . It is this K691 that likely stabilizes the negatively charged oxygen of the first mevaldyl-CoA intermediate. [1] The mevaldyl CoA intermediate is subsequently converted to Mavaldehyde with added stabilization from . It is then believed that the close proximity of increases the pKA of E559, allowing it to be a proton donor for the reduction of mevaldehyde into mevalonate.[1] Regulation of HMG-CoA Reductase As stated before, HMGR is among the most highly regulated enzymes in the human body.[2] Regulation of HMG-CoA reductase occurs at 4 different levels of feedback regulation. First by regulation of transcription of the reductase gene, which is activated by sterol regulatory element binding protein, a protein that binds to the promoter of the HMGR gene when cholesterol levels fall. The second level of regulation is at the translation of the HMGR mRNA, which is inhibited by Farnesol, a derivative of the mevalonate pathway.[2] The third level of HMGR regulation involves the degradation of intact reductase. As the level of sterols increases, HMGR reductase becomes more susceptible to ER-associated degradation. Helices 2-6 of the HMGR transmembrane domain, called the sterol-sensing domain, sense the increased levels of sterols. Degradation of HMGR is initiated when a membrane-bound cysteine protease cleaves residues within the transmembrane region of HMGR. Additionally, as sterol levels increase, the helices can expose Lysine 248 which can be ubiquitinated and subsequently trigger proteolytic degradation.[1][4] A final level of HMGR regulation is achieved by inhibition via . HMGR is phosphorylated and inactivated by an AMP-activated protein kinase, when the energy charge of the cell is low and AMP concentrations are high. Since Serine 872 is in the vicinity of the pohsphate of NADP, phosphorylation likely results in a decreased affinity for NADPH, halting the formation of Mevaldyl-CoA from HMG-CoA.[5]

Medical Implications

Comparison of Chemical Structure of HMG-CoA and Lovastatin

Crystal Structure of Human HMGR Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Elevated cholesterol levels have been identified as a major risk factor for coronary artery disease, the narrowing of arteries of the heart, which affected over 13 million people in the United States alone. It is a major cause of disability and death, killing over 500 thousand people in the USA in 2001. ^[6]

The statins are HMG-CoA reductase inhibitors. Discovered by Akira Endo in 1971, statins are similar in structure to HMG-CoA and act by competitively inhibiting HMGR. Since HMGR is the first committed enzyme in the cascade that eventually produces cholesterol, use of statins can dramatically reduce blood cholesterol levels.^[7] As a drug class, statins generated over $20 billion dollars in sales in 2009 with Pfizer’s Lipitor being the best selling drug in the world at the time of writing.^[8][9]

A number of crystal structures of HMGR with bound statins have been solved which elucidate how the statin molecule is bound by HMGR. Statins in general occupy the active site of HMGR, preventing HMG-CoA from binding. The structure of HMGR with bound statins () shows that the cis loop forms a number of polar interactions with the statin inhibitor, particularly residues Ser 684, Asp 690, Lys 691, Lys 692, and hydrogen bond interactions between Glu 559 and Asp 767 with the O5-hydroxyl of the statins. Van der Waals interactions between Leu 562, Val 683, Leu 853, Ala 856, and Leu 857 of HMGR and hydrophobic ring structures of the statins contribute to binding as well.^[10] These interactions result in the statins binding to HMGR with a K_i of between .1-2.3nM while the Michaelis constant K_M for HMG-CoA is 4uM, allowing the statins to outcompete HMG-CoA in binding to HMGR.^[11] Additional structures of HMGR with the statins , , , , and highlight the important residues involved in inhibitor binding.

Additional 3D Structures of HMG-CoA Reductase

3cct, 3ccw, 3ccz, 3cd0, 3cd5, 3cd7, 3cda, 3cdb – HMG-CoA Reductase Catalytic Domain
2qil – HMG-CoA Reductase Catalytic Domain
2q6b, 2q6c – Catalytic Domain of HMG-CoA Reductase
1t02 – Crystal Structure of Statin Bound HMG-CoA Reductase
1r31 – Crystal Structure of HMGR from Pseudomonas mevalonii
1hw8, 1hw9, 1hwi, 1hwj, 1hwk, 1hwl – HMG CoA Reductase with Various Statins Bound
1qax, 1qay – Ternary Complex of Pseudomonas Mevalonii HMGR with mevalonate

Additional Resources

• See: Pharmaceutical Drug Targets For Additional Information about Drug Targets for Related Diseases
• See: Metabolic Disorders For Additional Information.

References

1. ↑ ^{1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8} Roitelman J, Olender EH, Bar-Nun S, Dunn WA Jr, Simoni RD. Immunological evidence for eight spans in the membrane domain of 3-hydroxy-3-methylglutaryl coenzyme A reductase: implications for enzyme degradation in the endoplasmic reticulum. J Cell Biol. 1992 Jun;117(5):959-73. PMID:1374417
2. ↑ ^{2.0 2.1 2.2} Meigs TE, Roseman DS, Simoni RD. Regulation of 3-hydroxy-3-methylglutaryl-coenzyme A reductase degradation by the nonsterol mevalonate metabolite farnesol in vivo. J Biol Chem. 1996 Apr 5;271(14):7916-22. PMID:8626470
3. ↑ Istvan ES, Deisenhofer J. Structural mechanism for statin inhibition of HMG-CoA reductase. Science. 2001 May 11;292(5519):1160-4. PMID:11349148 doi:10.1126/science.1059344
4. ↑ Song BL, Sever N, DeBose-Boyd RA. Gp78, a membrane-anchored ubiquitin ligase, associates with Insig-1 and couples sterol-regulated ubiquitination to degradation of HMG CoA reductase. Mol Cell. 2005 Sep 16;19(6):829-40. PMID:16168377 doi:10.1016/j.molcel.2005.08.009
5. ↑ Goldstein JL, Brown MS. Regulation of the mevalonate pathway. Nature. 1990 Feb 1;343(6257):425-30. PMID:1967820 doi:http://dx.doi.org/10.1038/343425a0
6. ↑ www.nhlbi.nih.gov/health/.../Diseases/.../CAD_WhatIs.html
7. ↑ Endo A, Kuroda M, Tanzawa K. Competitive inhibition of 3-hydroxy-3-methylglutaryl coenzyme A reductase by ML-236A and ML-236B fungal metabolites, having hypocholesterolemic activity. FEBS Lett. 1976 Dec 31;72(2):323-6. PMID:16386050
8. ↑ http://www.drugs.com/top200.html
9. ↑ http://www.medicalnewstoday.com/articles/25046.php
10. ↑ Istvan ES, Deisenhofer J. Structural mechanism for statin inhibition of HMG-CoA reductase. Science. 2001 May 11;292(5519):1160-4. PMID:11349148 doi:10.1126/science.1059344
11. ↑ Corsini A, Maggi FM, Catapano AL. Pharmacology of competitive inhibitors of HMG-CoA reductase. Pharmacol Res. 1995 Jan;31(1):9-27. PMID:7784310