Protein Family Models

Date:

2024-08-14

Date:

2024-08-14

Malectin is a membrane-anchored protein of the endoplasmic reticulum that recognises and binds Glc2-N-glycan. It carries a signal peptide from residues 1-26, a C-terminal transmembrane helix from residues 255-274, and a highly conserved central part of approximately 190 residues followed by an acidic, glutamate-rich region. Carbohydrate-binding is mediated by the four aromatic residues, Y67, Y89, Y116, and F117 and the aspartate at D186. NMR-based ligand-screening studies has shown binding of the protein to maltose and related oligosaccharides, on the basis of which the protein has been designated "malectin", and its endogenous ligand is found to be Glc2-high-mannose N-glycan [1]. [1]. 18524852. Malectin: a novel carbohydrate-binding protein of the endoplasmic reticulum and a candidate player in the early steps of protein N-glycosylation. Schallus T, Jaeckh C, Feher K, Palma AS, Liu Y, Simpson JC, Mackeen M, Stier G, Gibson TJ, Feizi T, Pieler T, Muhle-Goll C;. Mol Biol Cell. 2008;19:3404-3414. (from Pfam)

Date:

2024-10-16

E or 'early' set domains are associated with the catalytic domain of galactose oxidase at the C-terminal end. Galactose oxidase is an extracellular monomeric enzyme which catalyzes the stereospecific oxidation of a broad range of primary alcohol substrates, and possesses a unique mononuclear copper site essential for catalysing a two-electron transfer reaction during the oxidation of primary alcohols to corresponding aldehydes. The second redox active centre necessary for the reaction was found to be situated at a tyrosine residue. The C-terminal domain of galactose oxidase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end, and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family adopt a secondary structure consisting of a bundle of seven, mostly antiparallel, beta-strands surrounding a hydrophobic core. The 7 strands are arranged in 2 sheets, in a Greek-key topology [1]. This domain is found in sugar-utilising enzymes, such as galactose oxidase or chitinase [2-6]. [1]. 11698678. Crystal structure of the precursor of galactose oxidase: an unusual self-processing enzyme. Firbank SJ, Rogers MS, Wilmot CM, Dooley DM, Halcrow MA, Knowles PF, McPherson MJ, Phillips SE;. Proc Natl Acad Sci U S A. 2001;98:12932-12937. [2]. 11923309. Cyclomaltodextrinase, neopullulanase, and maltogenic amylase are nearly indistinguishable from each other. Lee HS, Kim MS, Cho HS, Kim JI, Kim TJ, Choi JH, Park C, Lee HS, Oh BH, Park KH;. J Biol Chem. 2002;277:21891-2189. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

This domain forms an insert in bacterial beta-glucosidases and is found in other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dictyostelium prespore-cell-inducing factor Psi and in fibrocystin, the mammalian protein whose mutation leads to polycystic kidney and hepatic disease. The crystal structure of PA shows that this domain (named PA14 after its location in the PA20 pro-peptide) has a beta-barrel structure. The PA14 domain sequence suggests a binding function, rather than a catalytic role. The PA14 domain distribution is compatible with carbohydrate binding. [1]. 15236739. The PA14 domain, a conserved all-beta domain in bacterial toxins, enzymes, adhesins and signaling molecules. Rigden DJ, Mello LV, Galperin MY;. Trends Biochem Sci. 2004;29:335-339. (from Pfam)

Date:

2024-10-16

The kelch motif was initially discovered in Kelch (Swiss:Q04652). In this protein there are six copies of the motif. It has been shown that Swiss:Q04652 is related to Galactose Oxidase [1] for which a structure has been solved [2]. The kelch motif forms a beta sheet. Several of these sheets associate to form a beta propeller structure as found in Pfam:PF00064, Pfam:PF00400 and Pfam:PF00415. [1]. 8126718. Drosophila kelch motif is derived from a common enzyme fold. Bork P, Doolittle RF;. J Mol Biol 1994;236:1277-1282. [2]. 2002850. Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase. Ito N, Phillips SE, Stevens C, Ogel ZB, McPherson MJ, Keen JN, Yadav KD, Knowles PF;. Nature 1991;350:87-90. [3]. 15475350. Crystal structure of the Kelch domain of human Keap1. Li X, Zhang D, Hannink M, Beamer LJ;. J Biol Chem 2004;279:54750-54758. (from Pfam)

Date:

2024-10-16

This is a family of distinct cytochrome c peroxidases (CCPs) that contain two haem groups. Similar to other cytochrome c peroxidases, they reduce hydrogen peroxide to water using c-type haem as an oxidisable substrate. However, since they possess two, instead of one, haem prosthetic groups, bacterial CCPs reduce hydrogen peroxide without the need to generate semi-stable free radicals. The two haem groups have significantly different redox potentials. The high potential (+320 mV) haem feeds electrons from electron shuttle proteins to the low potential (-330 mV) haem, where peroxide is reduced (indeed, the low potential site is known as the peroxidatic site) [1]. The CCP protein itself is structured into two domains, each containing one c-type haem group, with a calcium-binding site at the domain interface. This family also includes MauG proteins, whose similarity to di-haem CCP was previously recognised [2]. [1]. 8591033. Crystal structure of the di-haem cytochrome c peroxidase from Pseudomonas aeruginosa. Fulop V, Ridout CJ, Greenwood C, Hajdu J;. Structure 1995;3:1225-1233. [2]. 9202457. Organization of methylamine utilization genes (mau) in 'Methylobacillus flagellatum' KT and analysis of mau mutants. Gak ER, Tsygankov YD, Chistoserdov AY;. Microbiology 1997;143:1827-1835. (from Pfam)

Date:

2024-10-16

The kelch motif was initially discovered in Kelch (Swiss:Q04652). In this protein there are six copies of the motif. It has been shown that Swiss:Q04652 is related to Galactose Oxidase [1] for which a structure has been solved [2]. The kelch motif forms a beta sheet. Several of these sheets associate to form a beta propeller structure as found in Pfam:PF00064, Pfam:PF00400 and Pfam:PF00415. [1]. 8126718. Drosophila kelch motif is derived from a common enzyme fold. Bork P, Doolittle RF;. J Mol Biol 1994;236:1277-1282. [2]. 2002850. Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase. Ito N, Phillips SE, Stevens C, Ogel ZB, McPherson MJ, Keen JN, Yadav KD, Knowles PF;. Nature 1991;350:87-90. [3]. 15475350. Crystal structure of the Kelch domain of human Keap1. Li X, Zhang D, Hannink M, Beamer LJ;. J Biol Chem 2004;279:54750-54758. (from Pfam)

Date:

2024-10-16

The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats [1]. The repeat lacks defined secondary structure [2]. [1]. 2430973. The structure of human thrombospondin, an adhesive glycoprotein with multiple calcium-binding sites and homologies with several different proteins. Lawler J, Hynes RO;. J Cell Biol 1986;103:1635-1648. [2]. 15014436. Structure of a thrombospondin C-terminal fragment reveals a novel calcium core in the type 3 repeats. Kvansakul M, Adams JC, Hohenester E;. EMBO J. 2004;23:1223-1233. (from Pfam)

Date:

2024-10-16