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Related Concept Videos

Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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The cadherins were one of the first cell adhesion molecules discovered; the term “cadherins”   is based on their calcium-dependent adhering properties. The first cadherins discovered on the epithelial, neuronal, and placental cells were named E-cadherin, P-cadherin, and N-cadherin, respectively. These classical cadherins share sequence and structural similarities. Other cadherins, including those involved in cell signaling, are grouped into non-classical cadherins. This...
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Starch-binding domains as CBM families-history, occurrence, structure, function and evolution.

Štefan Janeček1, Filip Mareček1, E Ann MacGregor2

  • 1Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, SK-84551 Bratislava, Slovakia; Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia.

Biotechnology Advances
|September 20, 2019
PubMed
Summary

Starch-binding domains (SBDs) are protein modules that help enzymes bind to raw starch. This review details their identification, structure, function, and evolution across various carbohydrate-binding module families.

Keywords:
Amylolytic enzymesCarbohydrate-binding module familiesEvolutionary relatednessRaw starch binding residuesβ-Sandwich fold

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Enzymology

Background:

  • Starch-binding domains (SBDs) are specialized carbohydrate-binding modules (CBMs) crucial for enzyme targeting to granular starch.
  • SBDs are integral to the CAZy database, with 15 families (e.g., CBM20, CBM21) exhibiting SBD characteristics.
  • These domains, typically ~100 residues with a β-sandwich fold, lack enzymatic activity but facilitate substrate binding.

Purpose of the Study:

  • To review the identification and classification of SBDs in amylolytic and other enzymes.
  • To detail the structural and functional characteristics of SBDs, including their position and copy number within proteins.
  • To explore the evolutionary relationships among SBD CBM families.

Main Methods:

  • Literature review of SBDs in amylolytic enzymes (CAZy GH families) and other proteins.
  • Analysis of SBD structural data, focusing on solved tertiary structures and ligand complexes.
  • Phylogenetic analysis of SBD CBM families.

Main Results:

  • Identification of 15 SBD-containing CBM families within the CAZy database.
  • Characterization of SBDs as ~100-residue modules with a β-sandwich fold and carbohydrate-binding sites.
  • Detailed structural and functional insights, including evolutionary relationships, for most SBDs.

Conclusions:

  • SBDs are diverse protein modules critical for starch recognition and enzyme targeting.
  • The review consolidates knowledge on SBDs, highlighting their structural conservation and functional importance.
  • Further research into novel SBDs and their roles in enzymatic processes is warranted.