| VOMI | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 crystal structure of vitelline membrane outer layer protein i (vmo-i): a folding motif with homologous greek key structures related by an internal three-fold symmetry | |||||||||
| Identifiers | |||||||||
| Symbol | VOMI | ||||||||
| Pfam | PF03762 | ||||||||
| InterPro | IPR005515 | ||||||||
| SCOP2 | 1vmo / SCOPe / SUPFAM | ||||||||
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In molecular biology, this entry refers to a protein domain called, the Vitelline membrane outer layer protein I (VMO-I). It is a structure found on the outside of an egg, in the vitelline membrane.
The major role of the vitelline membrane is to prevent the mixing of the yolk and albumen and also act as an important anti-microbial barrier, as indicated by the high content of lysozyme in the outer layer [1] Vitelline membrane outer layer protein I (VMO-I) binds tightly to ovomucin fibrils, which construct the backbone of the outer layer membrane. VMO-I has considerable activity to synthesize N-acetylchito-oligosaccharide from N-acetylglucosamine hexasaccharides but no hydrolysis activity. VMO-I is composed of 163 aa [2]
The structure [3] consists of three beta-sheets forming Greek key motifs, which are related by an internal pseudo three-fold symmetry. Furthermore, the structure of VOMI has strong similarity to the structure of the delta-endotoxin, as well as a carbohydrate-binding site in the top region of the common fold. [4] VMO-I revealed a unique structure of the P-prism fold, a new type of multi-sheet assembly.
The beta sheet, (β-sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in the formation of the fibrils and protein aggregates observed in amyloidosis, Alzheimer's disease and other proteinopathies.
The endoplasmic reticulum (ER) is, in essence, the transportation system of the eukaryotic cell, and has many other important functions such as protein folding. It is a type of organelle made up of two subunits – rough endoplasmic reticulum (RER), and smooth endoplasmic reticulum (SER). The endoplasmic reticulum is found in most eukaryotic cells and forms an interconnected network of flattened, membrane-enclosed sacs known as cisternae, and tubular structures in the SER. The membranes of the ER are continuous with the outer nuclear membrane. The endoplasmic reticulum is not found in red blood cells, or spermatozoa.
A transmembrane protein (TP) is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequently undergo significant conformational changes to move a substance through the membrane. They are usually highly hydrophobic and aggregate and precipitate in water. They require detergents or nonpolar solvents for extraction, although some of them (beta-barrels) can be also extracted using denaturing agents.
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The Rossmann fold is a tertiary fold found in proteins that bind nucleotides, such as enzyme cofactors FAD, NAD+, and NADP+. This fold is composed of alternating beta strands and alpha helical segments where the beta strands are hydrogen bonded to each other forming an extended beta sheet and the alpha helices surround both faces of the sheet to produce a three-layered sandwich. The classical Rossmann fold contains six beta strands whereas Rossmann-like folds, sometimes referred to as Rossmannoid folds, contain only five strands. The initial beta-alpha-beta (bab) fold is the most conserved segment of the Rossmann fold. The motif is named after Michael Rossmann who first noticed this structural motif in the enzyme lactate dehydrogenase in 1970 and who later observed that this was a frequently occurring motif in nucleotide binding proteins.
The zona pellucida is a specialized extracellular matrix that surrounds the plasma membrane of mammalian oocytes. It is a vital constitutive part of the oocyte. The zona pellucida first appears in unilaminar primary oocytes. It is secreted by both the oocyte and the ovarian follicles. The zona pellucida is surrounded by the corona radiata. The corona is composed of cells that care for the egg when it is emitted from the ovary.
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The vitelline membrane or vitelline envelope is a structure surrounding the outer surface of the plasma membrane of an ovum or, in some animals, the extracellular yolk and the oolemma. It is composed mostly of protein fibers, with protein receptors needed for sperm binding which, in turn, are bound to sperm plasma membrane receptors. The species-specificity between these receptors contributes to prevention of breeding between different species. It is called zona pellucida in mammals. Between the vitelline membrane and zona pellucida is a fluid-filled perivitelline space.
The TIM barrel, also known as an alpha/beta barrel, is a conserved protein fold consisting of eight alpha helices (α-helices) and eight parallel beta strands (β-strands) that alternate along the peptide backbone. The structure is named after triose-phosphate isomerase, a conserved metabolic enzyme. TIM barrels are ubiquitous, with approximately 10% of all enzymes adopting this fold. Further, five of seven enzyme commission (EC) enzyme classes include TIM barrel proteins. The TIM barrel fold is evolutionarily ancient, with many of its members possessing little similarity today, instead falling within the twilight zone of sequence similarity.
A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These tandem repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tightly sterically packed with leucine residues.
Voltage-dependent anion channels, or mitochondrial porins, are a class of porin ion channel located on the outer mitochondrial membrane. There is debate as to whether or not this channel is expressed in the cell surface membrane.
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Mycobacterial porins are a group of transmembrane beta-barrel proteins produced by mycobacteria, which allow hydrophilic nutrients to enter the bacterium. They are located in the impermeable mycobacterial outer membrane, or mycomembrane of fast-growing mycobacteria. The mycomembrane is unique and composed of very-long chain fatty acids, mycolic acids. These proteins are structurally different from the typical porins located in the outer membrane of Gram-negative bacteria. For example, the MspA protein forms a tightly interconnected octamer with eight-fold rotation symmetry that resembles a goblet and contains a central channel. Each protein subunit contains a beta-sandwich of immunoglobulin-like topology and a beta-ribbon arm that forms an oligomeric transmembrane beta-barrel.
BanLec is a lectin from the jacalin-related lectin family isolated from the fruit of the bananas Musa acuminata and Musa balbisiana. BanLec is one of the predominant proteins in the pulp of ripe bananas and has binding specificity for mannose and mannose-containing oligosaccharides. A 2010 study reported that BanLec was a potent inhibitor of HIV replication.
S-Adenosylmethionine synthetase, also known as methionine adenosyltransferase (MAT), is an enzyme that creates S-adenosylmethionine by reacting methionine and ATP.
In molecular biology, the vitamin B12-binding domain is a protein domain which binds to cobalamin. It can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain. Proteins containing the cobalamin-binding domain include:
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