Poly substrate binding domain

Poly(HASCL) depolymerases are able to bind to poly(3HB)-granules. This ability is specific because poly(3HB) depolymerases do not bind to chitin or to (crystalline) cellulose [56,57]. The poly(3HB)-binding ability is lost in truncated proteins which lack the C-terminal domain of about 60 amino acids, and these modified enzymes do not hydrolyze poly(3HB). However, the catalytic domain is unaffected since the activity with water-soluble oligomers of 3-hy-droxybutyrate or with artificial water-soluble substrates such as p-nitrophenyl-esters is unaffected [55, 56, 58, 59]. Obviously, the C-terminal domain of poly(3HB) depolymerases is responsible and sufficient for poly(3HB)-binding [poly(3HB)-binding domain]. These results are in agreement ... 

Fig. 4. Alignment of poly(HASCL) depolymerase C-terminal substrate binding domains. Two types of poly(HASCL) depolymerase C-terminal substrate binding domains (A and B) can be distinguished by amino acid alignment. Amino acids strictly conserved in all depolymerase proteins are indicated...

Kameshita, I., Matsuda, Z., Tanigushi, T., Shizuta, Y. (1984). Poly(ADP-ribose)synthetase. Separation and identification of three proteolytic fragments as the substrate-binding domain, the DNA binding domain, and the automodification domain. J. Biol. Chem. 259,4770-4776. 

Shin M, Yoshimoto H, Vacanti JP (2004) In vivo bone tissue engineering using mesenchymal stem cells on a novel electrospun nanofibrous scaffold. Tissue Eng 10 33-41 Shinomiya M, Iwata T, Doi Y (1998) The adsorption of substrate-binding domain of PHB depolymerases to the surface of poly(3-hydroxybutyric acid). Int J Biol Macromol 22 129-135 Sim YC, Sudesh K (Unpublished). Annual report 2009 (2009) http //www.simedaiby.com/ downloads/pdfs/SDB/Annual Report/Sime Darby AR2009.pdf. Accessed online. Accessed Oct 1 2010... 

Hiraishi T, Hirahara Y, Doi Y, Maeda M, Taguchi S (2006) Effects of mutations in the substrate-binding domain of poly[(/J)-3-hydroxybutyrate] (PHB) depolymerase from Ralstonia pickettii T1 on PHB degradation. Appl Environ Microbiol 72 7331-7338... 

Numata K, Sato S, Fujita M, Tsuge T, Iwata T, Doi Y (2007) Adsorption effects of poly(hydroxybutyric add) depolymerase on chain-folding surface of polyester single crystals revealed by mutant enzyme and frictional force microscopy. Polym Degrad Stab 92 176-183 Ohura T, Kasuya K, Doi Y (1999) Cloning and characterization of the polyhydroxybutyrate depolymerase gene of Pseudomonas stutzeri and analysis of the function of substrate-binding domains. Appl Environ Microbiol 65 189-197... 

Figure 7.4 Activation of PARP-1 by DNA breaks. PARP-1 is composed of three domains, DNA binding, automodification and catalytic (NAD+ binding) domains (1). In cells, PARP-1 localizes to nucleoli and actively transcribed regions of chromatin by interacting with RNA. When PARP-1 binds to DNA breaks, PARP-1 initiates the poly(ADP-ribosyl)ation reaction by using NAD+ as its substrate (2). PARP-1 itself is the main target of the poly(ADP-ribosyl)ation reaction. ADP-ribose polymers are formed on the automodification domain of PARP-1 (automodification). As a consequence of automodification, PARP-1 dissociates from DNA breaks (3). When cells are committed to apoptosis, PARP-1 is specifically cleaved by an apoptosisspecilic protease, caspase-3, resulting in the formation of a 24kDa N-terminal and 89 kDa C-terminal fragments (4). (see Color Plate 7)...

Poly(ADP-ribose) polymerase is a multifunctional, highly conserved enzyme in which three functional domains have been identified following limited proteolysis (Figure 4). These are a DNA binding domain, an automodification domain, and a catalytic domain, which includes the binding site for the substrate, NAD". ... 

Zhou et al. developed a novel aqueous thermoresponsive adsorbent material for DNA deposition. A 4-branched chain, starshaped copolymer was developed with each chain comprising a cationic poly(iV,iV-dimethylaminopropyl acrylamide] [PDMAPAAm] block forming the inner domain for DNA binding and a thermoresponsive poly(iV isopropylacrylamide] [PNIPAM] block, the most commonly used thermosensitive polymer, formed the outer domain for surface adsorption [42]. The copolymer and the luciferase-encoding plasmid DNA were complexed and polyplexes of size approximately 100 nm were obtained. The polyplex so formed exhibited LCST at 35°C and was deposited on the substrate by precipitation from an aqueous solution upon warming. Thus, enhancement in the transfection efficiency was observed. 

---