The Anatomy & Taxonomy of Protein Structure The Anatomy & Taxonomy of Protein Structure

III. Classification Of Proteins By Patterns Of Tertiary Structure

A. Summary of the Classification System

2. Outline of the Taxonomy

  1. Antiparallel α domains
    1. Up-and-down helix bundles
      • Myohemerythrin , hemerythrin
      • Cytochrome b562
      • Cytochrome c'
      • Uteroglobin
      • Staphylococcal protein A fragment
      • Influenza virus hemagglutinin "domain" around 3-fold
      • Tobacco mosaic virus protein
      • Cytochrome b5
      • Tyrosyl-tRNA synthetase domain 2
      • Ferritin (?) [yes]
      • Purple membrane protein (?) [yes]
    2. Greek key helix bundles
      • Myoglobin, hemoglobin
      • Thermolysin domain 2
      • T4 phage lysozyme domain 2
      • Papain domain 1
      • Cytochrome c peroxidase domain 1
    3. Miscellaneous antiparallel α
      • Carp muscle calcium-binding protein
      • Egg lysozyme
      • Citrate synthase
      • Catalase domain 2
      • Cytochrome c peroxidase domain 2
      • p-Hydroxybenzoate hydroxylase domain
  2. Parallel α/β domains
    1. Singly wound parallel β barrels
      • Triosephosphate isomerase
      • Pyruvate kinase domain 1
      • KDPG aldolase
    2. Doubly wound parallel β sheets
      1. Classic doubly wound β sheets
        • Lactate dehydrogenase domain 1
        • Alcohol dehydrogenase domain 2
        • Aspartate transcarbamylase catalytic domain 2
        • Phosphoglycerate kinase domain 1
        • Tyrosyl-tRNA synthetase domain 1(?)
        • Phosphorylase domain 2, central three layers
      2. Doubly wound variations
        • Glyceraldehyde-phosphate dehydrogenase domain 1
        • Phosphorylase domain 1, central three layers
        • Flavodoxin
        • Subtilisin
        • Arabinose-binding protein domains 1 and 2
        • Dihydrofolate reductase
        • Adenylate kinase
        • Rhodanese domains 1 and 2
        • Glutathione reductase domains 1 and 2
        • Phosphoglycerate mutase
        • Phosphoglycerate kinase domain 2
        • Pyruvate kinase domain 3
        • Hexokinase domains 1 and 2
        • Catalase domain 3
        • Aspartate aminotransferase
        • Aspartate transcarbamylase catalytic domain 1
        • Phosphofructokinase domain 1
        • p-Hydroxybenzoate hydroxylase domain 1
        • Glucosephosphate isomerase domain 1
        • Glutathione peroxidase
    3. Miscellaneous parallel α/β
      • Carboxypeptidase
      • Thioredoxin
      • Carbonic anhydrase
      • Phosphofructokinase domain 2
      • Glucosephosphate isomerase domain 2
  3. Antiparallel β domains
    1. Up-and-down β barrels
      • Papain domain 2
      • Soybean trypsin inhibitor
      • Catalase domain 1
    2. Greek key β barrels
      1. Simple Greek keys
        • Trypsin-like serine proteases domains 1 and 2
        • Pyruvate kinase domain 2
        • Prealbumin
        • Plastocyanin, azurin
        • Immunoglobulin, variable and constant domains
        • Cu,Zn superoxide dismutase
        • Staphylococcal nuclease
      2. "Jellyroll" Greek keys
        • Tomato bushy stunt virus protein domains 2 and 3
        • Southern bean mosaic virus protein
        • Concanavalin A
        • Influenza virus hemagglutinin HA1
        • γ-Crystallin domains 1 and 2
    3. Multiple, partial, and other β barrels
      • Acid proteases domains 1 and 2
      • Alcohol dehydrogenase domain 1
      • Pancreatic ribonuclease
    4. Open-face β sandwiches
      • T4 lysozyme domain 1
      • Aspartate transcarbamylase regulatory domains 1 and 2
      • Streptomyces subtilisin inhibitor
      • Glutathione reductase domain 3
      • Thermolysin domain 1
      • Glyceraldehyde-phosphate dehydrogenase domain 2
      • Bacteriochlorophyll protein
      • p-Hydroxybenzoate hydroxylase domain 2
      • Influenza virus hemagglutinin HA2
      • L7/L12 ribosomal protein
    5. Miscellaneous antiparallel β
      • Gene 5 protein, E. coli
      • Lactate dehydrogenase domain 2
      • Tomato bushy stunt virus protein "domain" 1
  4. Small disulfide-rich or metal-rich domains
    1. SS-rich
      1. Toxin-agglutinin fold
        • Erabutoxin, cobra neurotoxin
        • Wheat germ agglutinin domains 1, 2, 3, and 4
      2. Other SS-rich
        • Pancreatic trypsin inhibitor
        • Insulin
        • Phospholipase A2
        • Crambin
    2. Metal-rich
      1. Up-and-down ligand cages
        • Rubredoxin
        • Cytochrome b5
        • Cytochrome c
        • Cytochrome c3
      2. Greek key ligand cages
        • Ferredoxin
        • High-potential iron protein