Protein Family Models

Jacalin_like and EEP (endonuclease/exonuclease/phosphatase) domains-containing protein are a diverse group of proteins that play a variety of roles in cells.

Date:

2023-12-19

glycoside hydrolase family 97 protein with C-terminal Ricin-type beta-trefoil lectin domain

Date:

2023-12-01

This domain is found at the N-terminus of beta-1,3-glucan-binding proteins involved in recognition of invading micro-organisms. It often co-occurs with Pfam:PF00722 (Glycosyl hydrolases family 16). It recognises and binds to a triple-helical beta-1,3-glucan structure [1-2]. [1]. 19561300. Solution structure of the silkworm betaGRP/GNBP3 N-terminal. domain reveals the mechanism for beta-1,3-glucan-specific. recognition.. Takahasi K, Ochiai M, Horiuchi M, Kumeta H, Ogura K, Ashida M,. Inagaki F;. Proc Natl Acad Sci U S A. 2009;106:11679-11684.. [2]. 21697086. Structural insights into recognition of triple-helical. beta-glucans by an insect fungal receptor.. Kanagawa M, Satoh T, Ikeda A, Adachi Y, Ohno N, Yamaguchi Y;. J Biol Chem. 2011;286:29158-29165. (from Pfam)

Date:

2024-04-03

This is a mannan-specific carbohydrate binding domain, previously known as the X4 module [1]. Unlike other carbohydrate binding modules, binding to substrate causes a conformational change [2]. [1]. 15004012. X4 modules represent a new family of carbohydrate-binding. modules that display novel properties.. Bolam DN, Xie H, Pell G, Hogg D, Galbraith G, Henrissat B,. Gilbert HJ;. J Biol Chem. 2004;279:22953-22963.. [2]. 15740741. Structure of a mannan-specific family 35 carbohydrate-binding. module: evidence for significant conformational changes upon. ligand binding.. Tunnicliffe RB, Bolam DN, Pell G, Gilbert HJ, Williamson MP;. J Mol Biol. 2005;347:287-296. (from Pfam)

Date:

2024-04-03

CBM9_2 is a family of putative endoxylanase-like proteins that belong to the Carbohydrate-binding family 9. (from Pfam)

Date:

2023-12-12

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:

2024-04-03

This domain is found at the C terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose [1]. [1]. 17322304. A Tomato Endo-beta-1,4-glucanase, SlCel9C1, Represents a. Distinct Subclass with a New Family of Carbohydrate Binding. Modules (CBM49).. Urbanowicz BR, Catala C, Irwin D, Wilson DB, Ripoll DR, Rose JK;. J Biol Chem. 2007;282:12066-12074. (from Pfam)

Date:

2024-04-03

Members of this family are found in both fungi, bacteria and wood-eating arthropods. The domain is found at the N-terminus of rhamnogalacturonase B, a member of the polysaccharide lyase family 4. The domain adopts a structure consisting of a beta super-sandwich, with eighteen strands in two beta-sheets [1]. The three domains of the whole protein rhamnogalacturonan lyase (RGL4), are involved in the degradation of rhamnogalacturonan-I, RG-I, an important pectic plant cell-wall polysaccharide. The active-site residues are a lysine at position 169 in UniProtKB:Q00019 and a histidine at 229, Lys169 is likely to be a proton abstractor, His229 a proton donor in the mechanism. The substrate is a disaccharide, and RGL4, in contrast to other rhamnogalacturonan hydrolases, cleaves the alpha-1,4 linkages of RG-I between Rha and GalUA through a beta-elimination resulting in a double bond in the nonreducing GalUA residue, and is thus classified as a polysaccharide lyase (PL) [2]. [1]. 15135077. Rhamnogalacturonan lyase reveals a unique three-domain modular. structure for polysaccharide lyase family 4.. McDonough MA, Kadirvelraj R, Harris P, Poulsen JC, Larsen S;. FEBS Lett. 2004;565:188-194.. [2]. 20851126. Structural and biochemical studies elucidate the mechanism of. rhamnogalacturonan lyase from Aspergillus aculeatus.. Jensen MH, Otten H, Christensen U, Borchert TV, Christensen LL,. Larsen S, Leggio LL;. J Mol Biol. 2010;404:100-111. (from Pfam)

Date:

2024-04-03

This is a carbohydrate binding domain which has been shown in Schizosaccharomyces pombe to be required for septum localisation [1]. [1]. 18466295. The Schizosaccharomyces pombe endo-1,3-beta-glucanase Eng1. contains a novel carbohydrate binding module required for septum. localization.. Martin-Cuadrado AB, Del Dedo JE, de Medina-Redondo M, Fontaine. T, Del Rey F, Latge JP, de Aldana CR;. Mol Microbiol. 2008; [Epub ahead of print] (from Pfam)

Date:

2024-04-03

Fve is a major fruiting body protein from Flammulina velutipes, a mushroom possessing immunomodulatory activity. It stimulates lymphocyte mitogenesis, suppresses systemic anaphylaxis reactions and oedema, enhances transcription of IL-2, IFN-gamma and TNF-alpha, and haemagglutinates red blood cells. It appears to be a lectin with specificity for complex cell-surface carbohydrates. Fve adopts a tertiary structure consisting of an immunoglobulin-like beta-sandwich, with seven strands arranged in two beta sheets, in a Greek-key topology. It forms a non-covalently linked homodimer containing no Cys, His or Met residues; dimerisation occurs by 3-D domain swapping of the N-terminal helices and is stabilised predominantly by hydrophobic interactions [1]. [1]. 12948495. A 1.7A structure of Fve, a member of the new fungal. immunomodulatory protein family.. Paaventhan P, Joseph JS, Seow SV, Vaday S, Robinson H, Chua KY,. Kolatkar PR;. J Mol Biol. 2003;332:461-470. (from Pfam)

Date:

2024-04-03

This entry represents a domain found in prokaryotic alpha-amylase and 4-alpha-glucanotransferase. It adopts a beta-sandwich fold, in which two layers of anti-parallel beta-sheets are arranged in a nearly parallel fashion. The exact function of this family is, as yet, unknown, however it has been proposed that they may play a role in transglycosylation reactions [1]. [1]. 12618437. Crystal structures of 4-alpha-glucanotransferase from. Thermococcus litoralis and its complex with an inhibitor.. Imamura H, Fushinobu S, Yamamoto M, Kumasaka T, Jeon BS, Wakagi. T, Matsuzawa H;. J Biol Chem. 2003;278:19378-19386. (from Pfam)

Date:

2024-04-03

The H-type lectin domain is a unit of six beta chains, combined into a homo-hexamer. It is involved in self/non-self recognition of cells, through binding with carbohydrates [1]. It is sometimes found in association with the F5_F8_type_C domain Pfam:PF00754. [1]. 16704980. Biochemical and structural analysis of Helix pomatia agglutinin.. A hexameric lectin with a novel fold.. Sanchez JF, Lescar J, Chazalet V, Audfray A, Gagnon J, Alvarez. R, Breton C, Imberty A, Mitchell EP;. J Biol Chem. 2006;281:20171-20180. (from Pfam)

Date:

2024-04-03

CBM9_1 is a C-terminal domain on bacterial xylanase proteins, and it is tandemly repeated in a number of family-members. The CBM9 module binds to amorphous and crystalline cellulose and a range of soluble di- and monosaccharides as well as to cello- and xylo- oligomers of different degrees of polymerisation. Comparison of the glucose and cellobiose complexes during crystallisation reveals surprising differences in binding of these two substrates by CBM9-2. Cellobiose was found to bind in a distinct orientation from glucose, while still maintaining optimal stacking and electrostatic interactions with the reducing end sugar [1]. [1]. 11371186. Crystal structures of the family 9 carbohydrate-binding module. from Thermotoga maritima xylanase 10A in native and ligand-bound. forms.. Notenboom V, Boraston AB, Kilburn DG, Rose DR;. Biochemistry. 2001;40:6248-6256. (from Pfam)

Date:

2024-04-03

This probable domain is found in bacterial transcriptional regulators such as DeoR and SorC. These proteins have an amino-terminal helix-turn-helix Pfam:PF00325 that binds to DNA. This domain is probably the ligand regulator binding region. SorC is regulated by sorbose and other members of this family are likely to be regulated by other sugar substrates. (from Pfam)

Date:

2024-04-03

Domain is found in pullanase - carbohydrate de-branching - proteins. It is found both to the N or the C terminii of of the alpha-amylase active site region. This domain contains several conserved aromatic residues that are suggestive of a carbohydrate binding function. [1]. 12625841. New Knowledge from Old: In silico discovery of novel protein. domains in Streptomyces coelicolor.. Yeats C, Bentley S, Bateman A;. BMC Microbiol 2003;3:3-3. (from Pfam)

Date:

2024-04-03

Date:

2023-12-12

PapG, the adhesin of the P-pili, is situated at the tip and is only a minor component of the whole pilus structure. A two-domain structure has been postulated for PapG; a carbohydrate binding N-terminus (this domain) and chaperone binding C-terminus. The carbohydrate-binding domain interacts with the receptor glycan [1,2]. [1]. 11454740. The solution structure of PapGII from uropathogenic Escherichia. coli and its recognition of glycolipid receptors.. Sung MA, Fleming K, Chen HA, Matthews S;. EMBO Rep 2001;2:621-627.. [2]. 11440716. Structural basis of the interaction of the pyelonephritic E.. coli adhesin to its human kidney receptor.. Dodson KW, Pinkner JS, Rose T, Magnusson G, Hultgren SJ, Waksman. G;. Cell 2001;105:733-743. (from Pfam)

Date:

2024-04-03

This short domain is found in many different glycosyl hydrolase enzymes, representing the carbohydrate-binding module family 5/12, including proteins such as chitinase A1, chitinase B, and endoglucanase. The domain has a carbohydrate-binding function and contains six aromatic groups that may be important for binding. These modules have a core structure consisting of a 3-stranded meander beta-sheet [1-5]. [1]. 10788483. Solution structure of the chitin-binding domain of Bacillus. circulans WL-12 chitinase A1.. Ikegami T, Okada T, Hashimoto M, Seino S, Watanabe T, Shirakawa. M;. J Biol Chem. 2000;275:13654-13661.. Paper describing PDB structure 1wvu. [2]. 16516924. Structural studies of a two-domain chitinase from Streptomyces. griseus HUT6037.. Kezuka Y, Ohishi M, Itoh Y, Watanabe J, Mitsutomi M, Watanabe T,. Nonaka T;. J Mol Biol. 2006;358:472-484.. Paper describing PDB structure 2d49. [3]. 16567413. Identification of the substrate interaction region of the. chitin-binding domain of Streptomyces griseus chitinase C.. Akagi K, Watanabe J, Hara M, Kezuka Y, Chikaishi E, Yamaguchi T,. Akutsu H, Nonaka T, Watanabe T, Ikegami T;. J Biochem. 2006;139:483-493.DR CAZY; CBM5;. Paper describing PDB structure 2rts. [4]. 24272751. Solution structure of the chitin-binding domain 1 (ChBD1) of a. hyperthermophilic chitinase from Pyrococcus furiosus.. Mine S, Nakamura T, Sato T, Ikegami T, Uegaki K;. J Biochem. 2014;155:115-122.. [5]. 25479092. Structure-based analysis of domain function of chitin. oligosaccharide deacetylase from Vibrio parahaemolyticus.. Hirano T, Sugiyama K, Sakaki Y, Hakamata W, Park SY, Nishio T;. FEBS Lett.. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-04-03

Date:

2023-12-12

Two tryptophan residues are involved in cellulose binding. Cellulose binding domain found in bacteria. [1]. 7766609. Solution structure of a cellulose-binding domain from. Cellulomonas fimi by nuclear magnetic resonance spectroscopy.. Xu GY, Ong E, Gilkes NR, Kilburn DG, Muhandiram DR,. Harris-Brandts M, Carver JP, Kay LE, Harvey TS;. Biochemistry 1995;34:6993-7009. (from Pfam)

Date:

2024-04-03