Substrate binding domain

A linking domain, which links the catalytic domain with the substrate-binding domain. 

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...

All isoforms of PKC are predominantly localized to the cytosol and, upon activation, undergo translocation to either plasma or nuclear membranes. However, newly synthesized PKCs are localized to the plasmalemma and are in an open conformation in which the auto inhibitory pseudosubstrate sequence is removed from the substrate binding domain. The maturation of PKC isoforms is effected by phosphoinositide-dependentkinase-I (PDK-I), which phosphorylates a conserved threonine residue in the activation loop of the catalytic (C4) domain [24]. This in turn permits the autophosphorylation of C-terminus threonine and serine residues in PKC, a step which is a prerequisite for catalytic activity (see also Chs 22 and 23). The phosphorylated enzyme is then released into the cytosol, where it is maintained in an inactive conformation by the bound pseudosubstrate. It was originally thought that 3-phosphoinositides such as PI(3,4)P2 and PI(3,4,5)P3 could directly activate PKCs. However, it now seems more likely that these lipids serve to activate PDK-1 (a frequent contaminant of PKC preparations). 

It was initially argued that the best potential PTK inhibitors would be compounds that compete for the substrate in the kinase binding domain. It was argued that such compounds would be less toxic than ATP mimics since they bind to those domains at the kinase site that are less conserved than the substrate binding domains. Indeed tyrphostins like AG 490 which blocks Jak-2 [10] and AG 556 which possesses anti-inflammatory properties have been shown to be highly non-toxic in vivo [34-37]. 

Schrag, M.L. and Wienkers, L.C. (2001) Covalent alteration of the CYP3A4 active site evidence for multiple substrate binding domains. Archives of Biochemistry and Biophysics, 391 (1), 49-55. 

Fig. 2. An example of a complex multidomain protein that includes both domain concatenation and intercalation. (A) See color insert. RASMOL view of phosphotransferase pyruvate kinase (pdb entry lpkn) colored to show the three identifiable domains. Blue is the j3 barrel regulatory domain, orange is an eightfold a/fi barrel, the catalytic substrate binding domain, and green is a central /3, a/(B nucleotide binding domain. Not displayed is the leader subsequence composed of a random coil and short helix. (B) Linear order along the sequence of these components.

SCF -CyclinE-E2 complexes [66, 85, 103]. In all cases, no intermolecular collision was found in the final models. The substrate-binding domains of all three F-box proteins are positioned on the same side of the SCF complex as the E2. In addition, these domains are all oriented toward the E2 active site. Remarkably, the positions of the WD40 domain in the and SCF models are strikingly... 

The crystal structure of the peptide substrate-binding domain (140—245 of 517 residues of human al subunit) of the human type I enzyme forms 2.5 tetratricopeptide (TPR) repeat domains with five a helices (PDB accession number ITJC). The organization of tyrosine residues is suggested to be key to its interaction with the substrate peptide in a polyproline II helix. The TPR motif is composed of a 34 amino acid repeated a helical motif, and is typically involved in protein-protein interactions. The tandem repeats of TPR motifs are found in many proteins related to chaperone, cell cycle, transcription, and protein transport... 

Prolyl 4-hydroxylase alpha subunit substrate-binding domain (with 2.5 tetratricopeptide motifs) PDI a, a domain (active) W catalytic site -Cys-Gly-His-Cys-PDI b, b domain (inactive) PDI c region (higly acidic)... 

Figure 10 Schematic illustration of the posttranslational enzymes and related proteins. P4H a subunits have three isoforms. Each has three domains. The substrate-binding domain is in the middle. The catalytic domain is at the C-terminal end. Lysyl hydroxylase-3 (LH3) has two different catalytic activities. The N-terminal domain has the glucosyltransferase activity and the C-terminal domain has the hydroxylase activity. LH1 and LH2 also have similar domain structures but the glucosyltransferase activities are not detected in vitro.

Although its two domains could function independently, removal of the substrate-binding domain of ngCenA reduced enzymatic activity against microcrystalline cellulose but not against CMC or amorphous cellulose (12). This suggested that the substrate-binding domain played a critical role in the hydrolysis of crystalline cellulose. 

Hydration and/or dehydration reactions are frequently catalyzed by metallopro-teins. Examples are proteins containing nickel (urease), zinc (e.g., peptidases), molybdenum (the hydratase partial reaction of formate oxidoreductase), tungsten (acetylene hydratase). An obvious difference between Ni, Zn, on the one hand, and Fe, Mo, W, on the other, is that the first are directly coordinated to the protein whereas the latter are also part of a cofactor. With reference to the Fe/S cluster in aconitase it has been suggested that cofactor coordination may provide an added flexibility to the active site, in particular to the substrate binding domain [15],... 

The initial turnover number of the thioanisole oxidation by the reconstituted Mb is clearly larger than that observed for the native Mb, and the kcat/Km value is more than seven fold higher than that of the native protein. The epoxidation of styrene is also effectively catalyzed by the reconstituted Mb by 10-fold increase compared to native Mb. These findings indicate that the appropriate modification of the heme propionate side chains forms a substrate-binding domain that enhances the peroxidase and peroxygenase activities of Mb, as shown in Table VI. 

As mentioned above the specific structure of HP-RJ has a clear disadvantage for use as universal catalytic module. The substrate binding domain cannot be extended in the 5 direction, requiring HP-RJ to be placed exclusively at the 5 end of a multi-target ribozyme. To overcome this limitation we prepared the branched ribozyme HP-RJBR (Figure 5.2.10). 

Importance of substrate binding domains in hollocellulose degradation 207... 

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