Structural basis of functions of the mitochondrial cytochrome bc1 complex

AbstractThe crystal structure of the cytochrome bc1 complex (ubiquinol-cytochrome c reductase) from bovine heart submitochondria was determined at 2.9 Å resolution. The bc1 complex in crystal exists as a closely interacting dimer, suggesting that the dimer is a functional unit. Over half of the mass of the complex, including subunits core 1 and core 2, are on the matrix side of the membrane, while most of the cytochrome b subunit is located within the membrane. There are 13 transmembrane helices in each monomer, eight of them belonging to cytochrome b. Two large cavities are made of the transmembrane helices D, C, F and H in one monomer and helices D′ and E′ from the other monomer of cytochrome b, and the transmembrane helices of c1, iron-sulfur protein (ISP), and subunits 10 and 11. These cavities provide entrances for ubiquinone or inhibitor and connect the Qi pocket of one monomer and the Qo pocket of the other monomer. Ubiquinol made at the Qi site of one monomer can proceed to the nearby Qo site of the other monomer without having to leave the bc1 complex. The soluble parts of cytochrome c1 and ISP, including their redox prosthetic groups, are located on the cytoplasmic side of the membrane. The distances between the four redox centers in the complex have been determined, and the binding sites for several electron transfer inhibitors have been located. Structural analysis of the protein/inhibitor complexes revealed that the extramembrane domain of the Rieske iron-sulfur protein may undergo substantial movement during the catalytic cycle of the complex. The Rieske protein movement and the larger than expected distance between FeS and cytochrome c1 heme suggest that electron transfer reaction between FeS and cytochrome c1 may involve movements or conformational changes in the soluble domain of iron-sulfur protein. The inhibitory function of E-β-methoxyacrylate-stilbene and myxothiazol may result from the increase of mobility in ISP, whereas the function of stigmatellin and 5-undecyl-6-hydroxy-4,7-dioxobenzothiazole may result from the immobilization of ISP

Nonclassical binding of formylated peptide in crystal structure of the MHC class lb molecule H2-M3

AbstractH2-M3 is a class Ib MHC molecule of the mouse with a 104-fold preference for binding N-fonmylated peptides. To elucidate the basis of this unusual specificity, we expressed and crystallized a soluble form of M3 with a fonnylated nonamer peptide, fMYFINILTL, and determined the structure by X-ray crystallography. M3, refined at 2.1A˚resolution, resembles class la MHC molecules in its overall structure, but differs in the peptide-binding groove. The A pocket, which usually accommodates the free N-terminus of a bound peptide, is closed, and the peptide Is shifted one residue, such that the P1 side chain is lodged in the B pocket. The formyl group Is coordinated by His-9 and a bound water on the floor of the groove

Structure of the LDL receptor extracellular domain at endosomal pH

The low-density lipoprotein receptor mediates cholesterol homeostasis through endocytosis of lipoproteins. It discharges its ligand in the endosome at pH Ͻ 6. In the crystal structure at pH ϭ 5.3, the ligand-binding domain (modules R2 to R7) folds back as an arc over the epidermal growth factor precursor homology domain (the modules A, B, ␤ propeller, and C). The modules R4 and R5, which are critical for lipoprotein binding, associate with the ␤ propeller via their calcium-binding loop. We propose a mechanism for lipoprotein release in the endosome whereby the ␤ propeller functions as an alternate substrate for the ligand-binding domain, binding in a calcium-dependent way and promoting lipoprotein release. The low-density lipoprotein receptor (LDL-R) regulates cholesterol homeostasis in mammalian cells. LDL-R removes cholesterolcarrying lipoproteins from plasma circulation in a process known as receptor-mediated endocytosis (1). Ligands bound extracellularly by LDL-R at neutral pH are internalized and then released in the endosomes ( pH Ͻ 6), leading to their subsequent lysosomal degradation. The receptor then recycles to the cell surface. Mutations in the LDL-R gene cause familial hypercholesterolemia (FH), one of the most common simply inherited genetic diseases (2). FH heterozygotes exhibit a reduced rate of receptor-mediated removal of plasma LDL by the liver, ultimately leading to early onset coronary heart disease and atherosclerosis. More than 920 mutations in LDL-R are known, some of which have been functionally characterized (2, 3). The extracellular domain of LDL-R is composed of a "ligand-binding domain" (with cysteine-rich repeats R1 to R7) and an "epidermal growth factor (EGF) precursor homology domain" (with the EGF-like repeats A, B, and C, as well as a ␤ propeller between B and C) (4, 5). LDL-R binds LDL via the single protein in LDL, the 550-kD apolipoprotein B (apoB) (6); deleting R3, R4, R5, R6, or R7 reduces LDL binding to Ͻ20% of that of the wild-type LDL-R (7). LDL-R also binds to very low density lipoprotein (VLDL), ␤-VLDL, intermediate density lipoprotein (IDL), and chylomicron remnants via the 33-kD apolipoprotein E (apoE) (8, 9); disrupting R5 decreases ␤-VLDL binding to 30 to 50% of that of the wild-type receptor, whereas disrupting R4 or R6 reduces binding only slightly (7). At neutral pH, negative charges on repeats R1 to R7 are thought to interact with positive charges on apoB and apoE. Indeed, LDL binding to LDL-R can be disrupted competitively with polycations or permanently by selective chemical modification of positively charged residues on apoE or apoB Dissociation of ligands is crucial for receptor recycling and hence proper receptor function; mutations in LDL-R that impair ligand release produce FH (2). Deletion mutagenesis studies in LDL-R and the related VLDL-R have indicated that, although the ligand-binding domain is sufficient for binding lipoprotein particles, the receptor requires the EGF precursor homology domain for ligand release (16-18). The structural basis for LDL-R's ability to recognize a diverse group of lipoprotein particles, all varying in size, and release them at acidic pH is unknown. High-resolution crystal structures of modules R5 (12) and ␤ propeller-C (5) are known, and solution NMR structures are known for single and tandem repeats, including R1, R2, R5, R6, A, and B Structure determination. The extracellular domain of human LDL-R (residues 1 to 699) was crystallized at pH ϭ 5.3, with the symmetry of space group P3 1 21 (28). Soaking crystals in sodium 12-tungstophosphate (Na 3 PW 12 O 40 ) improved their diffractive quality and incorporated large anomalous scatterers. The asymmetric unit contains a single protein molecule and two tungsten clusters as well as half of a tungsten cluster on a crystallographic twofold axis. Data collection, structure determination, and model statistics are given in Monomer description. There is clear electron density in the crystal structure for the modules R2, R3, R4, R5, R6, R7, A, B, ␤ propeller, and C In the crystal, each monomer forms major contacts with five neighboring symmetry-related molecules. Although the relative orien

The Structure of the NPC1L1 N-Terminal Domain in a Closed Conformation

NPC1L1 is the molecular target of the cholesterol lowering drug Ezetimibe and mediates the intestinal absorption of cholesterol. Inhibition or deletion of NPC1L1 reduces intestinal cholesterol absorption, resulting in reduction of plasma cholesterol levels.Here we present the 2.8 Å crystal structure of the N-terminal domain (NTD) of NPC1L1 in the absence of cholesterol. The structure, combined with biochemical data, reveals the mechanism of cholesterol selectivity of NPC1L1. Comparison to the cholesterol free and bound structures of NPC1(NTD) reveals that NPC1L1(NTD) is in a closed conformation and the sterol binding pocket is occluded from solvent.The structure of NPC1L1(NTD) reveals a degree of flexibility surrounding the entrance to the sterol binding pocket, suggesting a gating mechanism that relies on multiple movements around the entrance to the sterol binding pocket

Proteins with leucine-rich repeats

Leucine-rich repeats are short sequence motifs present in over sixty proteins, all of which appear to be involved in protein-protein interactions. The crystal structure of ribonuclease inhibitor demonstrated that the repeats correspond to beta-alpha structural units. The recently determined crystal structure of the ribonuclease A-ribonuclease inhibitor complex suggests the basis for the protein-binding function of leucine-rich repeats

The leucine-rich repeat: a versatile binding motif

Leucine-rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. All proteins containing these repeats are thought to be involved in protein-protein interactions. The crystal structure of ribonuclease inhibitor protein has revealed that leucine-rich repeats correspond to β-α structural units. These units are arranged so that they form a parallel β-sheet with one surface exposed to solvent, so that the protein acquires an unusual, non-globular shape. These two features may be responsible for the protein-binding functions of proteins containing leucine-rich repeats

Crystallization and preliminary X-ray analysis of porcine ribonuclease inhibitor, a protein with leucine-rich repeats

Ribonuclease inhibitor was purified from pig liver and crystallized as 21°C from solutions containing dithiothreitol as an additive and ammonium sulfate, lithium sulfate or combinations of both as precipitants. Crystals have the symmetry of the tetragonal space group I4 with a = 134·9 Å and c = 83·6 Å, and diffract to better than 3 Å resolution. Self rotation functions and packing density of the crystals are consistent with two molecules in the asymmetric unit

Complex between bovine ribonuclease A and porcine ribonuclease inhibitor crystallizes in a similar unit cell as free ribonuclease inhibitor

We obtained three different morphologies of crystals of bovine ribonuclease A and porcine ribonuclease inhibitor. X-ray quality crystals were grown in 1·3 M ammonium sulfate, 100 mM sodium acetate (pH 5·0) and 20 mM dithiothreitol at 21°C. These crystals have the symmetry of the tetragonal space group I4 with a=133·3 Å and c =86·7 Å and diffract to 2·5 Å resolution; they have the same symmetry and only slightly different cell parameters than the crystals of free ribonuclease inhibitor. Polyacrylamide gel electrophoresis and the crystal density indicate that both ribonuclease inhibitor and ribonuclease A are present in the crystals. Although small, crystals are suitable for three-dimensional structural analysis