Proteins domain structures

CA Orengo, AD Michie, S Jones, DT Jones, MB Swindells, JM Thornton. CATH—A hierarchic classification of protein domain structures. Stnrcture 5 1093-1108, 1997. 

Antiparallel beta (P) structures comprise the second large group of protein domain structures. Functionally, this group is the most diverse it includes enzymes, transport proteins, antibodies, cell surface proteins, and virus coat proteins. The cores of these domains are built up by p strands that can vary in number from four or five to over ten. The P strands are arranged in a predominantly antiparallel fashion and usually in such a way that they form two P sheets that are joined together and packed against each other. 

Structure and Function of Peptidyl Carrier Protein Domains Structure and Function of Adenylation Domains Structure and Function of Condensation Domains Structure and Function of Thioesterase Domains Multidomain NRPS Structural Information PCP-C didomain structure PCP-TE didomain structure Structure of a C-A-PCP-TE termination module Pathways to Nonproteinogenic Amino Acids Incorporated into NRP Natural Nonproteinogenic Amino Acids Present as Cellular Metabolites Modification of Proteinogenic Amino Acids Nonproteinogenic Amino Acids Derived from Multistep Pathways Tailoring Enzymology in NRP Natural Products Chemical Approaches Toward Mechanistic Probes and Inhibitors of NRPS... 

Daniel-Vedele, F., Dorbe, M.F., Caboche, M. Rouze, P. (1989). Cloning and analysis of the tomato nitrate reductase-encoding gene protein domain structure and amino acid homologies in higher plants. Gene 85, 371-80. 

The CATH protein domain database (http //www.biochem.ucl.ac.uk/bsm/cath) is a hierarchical classification of protein domain structures into evolutionary families and structural groupings depending on sequence and structure similarity (Pearl et al, 2000). The protein domains are classified according to four major levels. 

Figure 13.1. Structural classes of protein folds, showing how the folds can be classified into different structural classes. Top row the three basic fold classes a, containing only a helices a and p, containing a helices and p sheets and p, containing only p sheets. Middle row three different architectural subclasses of the a and p class triosephosphate isomerase (TIM) barrel, three-layer sandwich, and roll. Bottom row two different arrangements of the "three-layer sandwich . The spiral conformations are the a helices, and the broad arrows are the p sheets. (From Orengo, C. A., Michie, A. D., Jones, S. et al. [1997]. CATH - a hierarchic classification of protein domain structures [Figure 2]. Structure, 5, 1093-108. Copyright 1997, Elsevier Science. Reprinted with permission.)...

Orengo, C. A., Michie, A. D., Jones, S. et al. (1997). CATH - a hierarchic classification of protein domain structures. Structure. 5(8), 1093-108. See cathwww.biochem.ucl.ac.uk/latest/index.html. 

Enabling the automated annotation of protein domain structure databases like PFAM and SMART contain HMMER models and curated alignments of known domains. These models can be used to specify a putative domain structure for novel protein query sequences. 

Integral proteins are embedded in the membrane itself, to some degree, and are referred to as transmembrane proteins if they extend from one side of the membrane to the other. Typically these proteins have multiple domains or regions that are either primarily hydrophobic, if embedded in the lipid bilayer, or hydrophilic if localized in the extra- or intracellular environment. More complicated tertiary and quaternary protein domain structures allow for the formation of channels or pores where appropriate arrangement of hydrophilic and hydrophobic amino acids on the internal surface of each channel or pore dictates which molecules may enter or bind for subsequent translocation from one side of the membrane to the other. Based on this, some proteins exhibit considerable substrate specificity (e.g., GLUTl a glucose transporter Scheepers et al., 2004) whereas others appear much less specific (e.g., P-glycoprotein Leslie et al., 2005). 

However, other perspectives suggest that there are likely to be as yet unidentified protein folds. As of 2004, the Pfam database (version 10.0) contained 6190 domains only about a third were associated with a protein of known structure. Some of these may be cases in which highly divergent or completely unrelated sequences adopt an already discovered fold. Some may not be amenable to structural characterization, either because they are too large for characterization by nuclear magnetic resonance spectroscopy (NMR), or contain disordered regions that interfere with crystallization. However, there may indeed be unidentified protein domain structures remaining to be discovered. 

Qrengo, C.A., et al. GATH—A hierarchic classification of protein domain structures. Structure 1997, 5(8), 1093-108. 

CATH http //www/biochem.ucl.ac.uk/bsm/cath new Protein domain structures... 

Evolutionary genomics involves the relationship between protein domains (structural or functional units in a protein) and analyzes the relationships between lower organisms and man. Some 50% of the human genome is thought to result from the sharing or shuffling of protein domains of lower organisms. For example, Li et al. ° count 1,865, 1,218, 1,183 and 973 domain types in human, fruitfly, nematode and yeast, respectively. ... 

Structure, 5,1093 (1997). CATH A Hierarchic Classification of Protein Domain Structures. 

It made a versatile chemical called PLP that comes from vitamin B6. K. M. Kim et al. Protein domain structure uncovers the origin of aerobic metabolism and the rise of planetary oxygen. 2012. Structure 20(1), p. 67. DOl 10.1016/j.str.2011.11.003. 

This group of proteins is ubiquitous. Most of the iron-sulfur proteins transfer electrons at negative redox potentials, e.g. in the respiratory chain or in photosynthesis, but some possess enzymatic, sensing or regulatory activity and they can also be involved in stabilization of protein domain structures or in radical formation. The important role of the element combination iron and sulfur in biology derives from many factors including availability, solubility and reactivity. The role of the sulfur ligands has been reviewed recently. For more reviews of various EPR-related aspects the reader is referred to the earlier report in this series. 

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