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Visualizing protein substructures

In this section, you will investigate the evolutionary conservation of protein substructures such as enzymatic catalytic sites. You will use publicly available online databases in addition to VMD to analyze the structures of two peroxidase enzymes and understand different methods of classifying related protein structures.

Structurally classifying proteins

There are many classification systems for grouping similar protein structures within the PDB. The Enzyme Commission (EC) nomenclature classifies enzyme structures by their catalytic function into 4 increasingly specific levels. The heme-dependent peroxidases that you will investigate are a family of enzymes found in plants, fungi, and animals and the 4-part hierarchical EC number of the family is 1.11.1.7.

Understanding ec classification

Start by visiting the PDB and searching for "1.11.1.7". Your search will reveal many structure entries in the PDB that belong to the EC family of heme-dependent peroxidases, such as myeloperoxidases and lactoperoxidases found in higher animals. Click on the "EC" icon (a small, white circular icon near the EC number for each entry) for one of the entries in the search results; this will take you to a description of EC 1.11.1.7. The EC number page provides information on principal references for the family, alternative names for enzymes in the family, and links to additional enzymatic databases such as BRENDA and KEGG. At the bottom of the page, you will see links to higher-level EC classifications such as "EC 1.11.1", "EC 1.11", and "EC 1". Visit each of the pages to understand the more general functional classes to which EC 1.11.1.7 belongs. For example, EC 1.11.1 contains many different families of peroxidases including and in addition to EC 1.11.1.7. Q5 : name 2 other peroxidase families from EC "1.11.1".

Visit the page for EC 1 (link at the bottom of the EC 1.11.1.7 page). EC 1 is the most general level of functional classification for the heme-dependent peroxidases. There are 6 major EC classifications including EC 1 (EC 1,2,3,4,5, and 6) and the heme-dependent peroxidases belong to the top-level classification of Oxidoreductases.

Understanding cath and scop classification

Return back to the PDB and search for entry 1CXP which will be a human myeloperoxidase belonging to EC 1.11.1.7. The PDB entry page for 1CXP lists additional structural classification data about the enzyme at the bottom of the page. Scroll down to the section titled "SCOP Classification". The Structural Classification Of Proteins (SCOP) is another system for categorizing protein structures that, like the EC system, uses a four level hierarchic system. The four SCOP levels correspond to structural class, fold, superfamily, and family. The superfamily of 1CXP as defined by SCOP is listed as "myeloperoxidase-like". Below the SCOP for 1CXP is the CATH structural classification information for the enzyme. CATH stands for Class (C) Architecture (A) Topology (T) Homologous superfamily (H) and provides an additional classification scheme for the structure. The class and architecture classification for 1CXP as defined by CATH are "mainly alpha" and "orthogonal bundle" respectively. The CATH class describes the major secondary structure composition of the enzyme, and therefore "mainly alpha" indicates that 1CXP is composed primarily of alpha helices.

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Source:  OpenStax, Geometric methods in structural computational biology. OpenStax CNX. Jun 11, 2007 Download for free at http://cnx.org/content/col10344/1.6
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