User:Eran Hodis/Sandbox3

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. ^[1] HMGR contains 8 transmembrane domains that have yet to be successfully crystallized, which anchor the protein to the membrane of the endoplasmic reticulum. ^[2] The catalytic portion of human HMGR forms a tetramer, with the individual monomers winding around each other. ^[2] 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. ^[2] Salt bridges between residues R641 and E782 as well as between E700 and E700 on neighboring monomers compliment the largely hydrophobic dimer-dimer interface. ^[2]

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. ^[2]

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. ^[2] 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. ^[2]

Regulation of HMG-CoA Reductase

As stated before, HMGR is among the most highly regulated enzymes in the human body.^[3] 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.^[3]

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.^[2][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]

Introduction

The nucleosome core particle contains two copies of each histone protein (H2A, H2B, H3 and H4) and 146 basepairs (bp) of superhelical DNA wrapped around this histone octamer. It represents the first order of DNA packaging in the nucleus and as such is the principal structure that determines DNA accessibility.

The Histone Octamer

Two copies of each histone protein, H2A, H2B, H3, and H4, are assembled into an octameric disc. Although each monomer has an N-terminal tail that projects from the histone core, the structure at left shows only a single tail from one H3 monomer.

All four histone proteins share a highly similar structural motif, the histone fold, comprising three alpha helices connected by two loops (shown here for H2A):

alpha1-loop1-alpha2-loop2-alpha3