Protein Family Models

This entry represents the PKD domain of Dyslexia-associated protein KIAA0319-like protein, in which it is found in four copies. This entry also includes Kunitz-type protease inhibitor 1 and LRP11 from human. Paper describing PDB structure 2c26. [1]. 16314409. Xyloglucan is recognized by carbohydrate-binding modules that interact with beta-glucan chains. Najmudin S, Guerreiro CI, Carvalho AL, Prates JA, Correia MA, Alves VD, Ferreira LM, Romao MJ, Gilbert HJ, Bolam DN, Fontes CM;. J Biol Chem. 2006;281:8815-8828. Paper describing PDB structure 2y3u. [2]. 21947205. Structure of collagenase G reveals a chew-and-digest mechanism of bacterial collagenolysis. Eckhard U, Schonauer E, Nuss D, Brandstetter H;. Nat Struct Mol Biol. 2011;18:1109-1114. Paper describing PDB structure 2yhg. [3]. 21905122. Ab initio phasing of a nucleoside hydrolase-related hypothetical protein from Saccharophagus degradans that is associated with carbohydrate metabolism. Hehemann JH, Marsters C, Boraston AB;. Proteins. 2011;79:2992-2998. Paper describing PDB structure 2z4t. [4]. 17962295. Crystal structure of Vibrionaceae Photobacterium sp. JT-ISH-224 alpha2,6-sialyltransferase in a ternary complex with donor product CMP and acceptor substrate lactose: catalytic mechanism and substrate recognition. Kakuta Y, Okino N, Kajiwara H, Ichikawa M, Takakura Y, Ito M, Yamamoto T;. Glycobiology. 2008;18:66-73. Paper describing PDB structure 4aqo. [5]. 23703618. Structural basis for activity regulation and substrate preference of clostridial collagenases G, H, and T. Eckhard U, Schonauer E, Brandstetter H;. J Biol Chem. 2013;288:20184-20194. (from Pfam)

Date:

2024-10-21

This entry represents a wide variety of bacterial Ig domains. [1]. 21606337. Structure of a bacterial cell surface decaheme electron conduit. Clarke TA, Edwards MJ, Gates AJ, Hall A, White GF, Bradley J, Reardon CL, Shi L, Beliaev AS, Marshall MJ, Wang Z, Watmough NJ, Fredrickson JK, Zachara JM, Butt JN, Richardson DJ;. Proc Natl Acad Sci U S A. 2011;108:9384-9389. (from Pfam)

Date:

2024-10-16

This domain is found in a number of bacterial chitinases and similar viral proteins. It is organised into a fibronectin III module domain-like fold, comprising only beta strands. Its function is not known, but it may be involved in interaction with the enzyme substrate, chitin [1,2]. It is separated by a hinge region from the catalytic domain (Pfam:PF00704); this hinge region is probably mobile, allowing the N-terminal domain to have different relative positions in solution [1]. [1]. 7704527. Crystal structure of a bacterial chitinase at 2.3 A resolution. Perrakis A, Tews I, Dauter Z, Oppenheim AB, Chet I, Wilson KS, Vorgias CE;. Structure 1994;2:1169-1180. [2]. 9377712. Evolution of immunoglobulin-like modules in chitinases: their structural flexibility and functional implications. Perrakis A, Ouzounis C, Wilson KS;. Fold Des 1997;2:291-294. (from Pfam)

Date:

2024-10-16

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. 2015;589:145-15. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-10-16

Date:

2024-08-14