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Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with lysozymes
Biology and Chemistry Report
4A8B
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/HYDROLASE
    Text HYDROLASE-HYDROLASE COMPLEX, CHAPERONE

    Polymeric Molecules

    Chain A,B,C,D,E,F,G,H,I,J,K,L
    Description PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ 
    Mutation YES 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 45543.2 
    Source Method genetically manipulated  
    Entity Name PROTEASE DO, DEGQ 
    Chain M,N,O,P,Q,R
    Description LYSOZYME C 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 14331.2 
    Source Method natural source  
    Entity Name 1,4-BETA-N-ACETYLMURAMIDASE C, ALLERGEN GAL D IV, GAL D 4 

     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D,E,F,G,H,I,J,K,L DEGQ_ECOLI P39099     
    M,N,O,P,Q,R LYSC_CHICK P00698     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B C D E F G H I J K L  3.4.21.107      
    M N O P Q R  3.2.1.17      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D,E,F,G,H,I,J,K,L
    GO ID   Ontology GO Term Definition
    6508   Proteolysis  The Hydrolysis of Proteins Into Smaller Polypeptides And/or Amino Acids by Cleavage of Their Peptide Bonds. 
    6950   Response to Stress  Any Process That Results in a Change in State or Activity of a Cell or an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Disturbance in Organismal or Cellular Homeostasis Usually But Not Necessarily Exogenous (e.g. Temperature Humidity Ionizing Radiation). 
    51603   Proteolysis Involved in Cellular Protein Catabolic Process  The Hydrolysis of a Peptide Bond or Bonds Within a Protein As Part of the Chemical Reactions and Pathways Resulting in the Breakdown of a Protein by Individual Cells. 
    42597   Periplasmic Space  The Region Between the Inner (cytoplasmic) and Outer Membrane (gram Negative Bacteria) or Cytoplasmic Membrane and Cell Wall (fungi and Gram Positive Bacteria). 
    71575   Integral Component of External Side of Plasma Membrane  The Component of the Plasma Membrane Consisting of the Gene Products Having Some Part That Penetrates the Membrane Bilayer with the Bulk Residing On the External Side of the Membrane. 
    3824   Catalytic Activity  Catalysis of a Biochemical Reaction At Physiological Temperatures. in Biologically Catalyzed Reactions the Reactants Are Known As Substrates and the Catalysts Are Naturally Occurring Macromolecular Substances Known As Enzymes. Enzymes Possess Specific Binding Sites For Substrates and Are Usually Composed Wholly or Largely of Protein But RNA That Has Catalytic Activity (ribozyme) Is Often Also Regarded As Enzymatic. 
    4252   Serine Type Endopeptidase Activity  Catalysis of the Hydrolysis of Internal Alpha Peptide Bonds in a Polypeptide Chain by a Catalytic Mechanism That Involves a Catalytic Triad Consisting of a Serine Nucleophile That Is Activated by a Proton Relay Involving an Acidic Residue (e.g. Aspartate or Glutamate) and a Basic Residue (usually Histidine). 
    8233   Peptidase Activity  Catalysis of the Hydrolysis of a Peptide Bond. a Peptide Bond Is a Covalent Bond Formed When the Carbon Atom From the Carboxyl Group of One Amino Acid Shares Electrons with the Nitrogen Atom From the Amino Group of a Second Amino Acid. 
    8236   Serine Type Peptidase Activity  Catalysis of the Hydrolysis of Peptide Bonds in a Polypeptide Chain by a Catalytic Mechanism That Involves a Catalytic Triad Consisting of a Serine Nucleophile That Is Activated by a Proton Relay Involving an Acidic Residue (e.g. Aspartate or Glutamate) and a Basic Residue (usually Histidine). 
    16787   Hydrolase Activity  Catalysis of the Hydrolysis of Various Bonds E.g. C O C N C C Phosphoric Anhydride Bonds Etc. Hydrolase Is the Systematic Name For Any Enzyme of EC Class 3. 
    42802   Identical Protein Binding  Interacting Selectively and Non Covalently with an Identical Protein or Proteins. 
    Chain M,N,O,P,Q,R
    GO ID   Ontology GO Term Definition
    1895   Retina Homeostasis  A Tissue Homeostatic Process Involved in the Maintenance of an Internal Equilibrium Within the Retina of the Eye Including Control of Cellular Proliferation and Death and Control of Metabolic Function. 
    8152   Metabolic Process  The Chemical Reactions and Pathways Including Anabolism and Catabolism by Which Living Organisms Transform Chemical Substances. Metabolic Processes Typically Transform Small Molecules But Also Include Macromolecular Processes Such As DNA Repair and Replication and Protein Synthesis and Degradation. 
    16998   Cell Wall Macromolecule Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Macromolecules That Form Part of a Cell Wall. 
    19835   Cytolysis  The Rupture of Cell Membranes and the Loss of Cytoplasm. 
    42742   Defense Response to Bacterium  Reactions Triggered in Response to the Presence of a Bacterium That Act to Protect the Cell or Organism. 
    5576   Extracellular Region  The Space External to the Outermost Structure of a Cell. For Cells Without External Protective or External Encapsulating Structures This Refers to Space Outside of the Plasma Membrane. This Term Covers the Host Cell Environment Outside an Intracellular Parasite. 
    5615   Extracellular Space  That Part of a Multicellular Organism Outside the Cells Proper Usually Taken to Be Outside the Plasma Membranes and Occupied by Fluid. 
    70062   Extracellular Vesicular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. 
    3796   Lysozyme Activity  Catalysis of the Hydrolysis of the Beta (1 >4) Linkages Between N Acetylmuramic Acid and N Acetyl D Glucosamine Residues in a Peptidoglycan and Between N Acetyl D Glucosamine Residues in Chitodextrins. 
    3824   Catalytic Activity  Catalysis of a Biochemical Reaction At Physiological Temperatures. in Biologically Catalyzed Reactions the Reactants Are Known As Substrates and the Catalysts Are Naturally Occurring Macromolecular Substances Known As Enzymes. Enzymes Possess Specific Binding Sites For Substrates and Are Usually Composed Wholly or Largely of Protein But RNA That Has Catalytic Activity (ribozyme) Is Often Also Regarded As Enzymatic. 
    5515   Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    16787   Hydrolase Activity  Catalysis of the Hydrolysis of Various Bonds E.g. C O C N C C Phosphoric Anhydride Bonds Etc. Hydrolase Is the Systematic Name For Any Enzyme of EC Class 3. 
    16798   Hydrolase Activity Acting On Glycosyl Bonds  Catalysis of the Hydrolysis of Any Glycosyl Bond. 
    42802   Identical Protein Binding  Interacting Selectively and Non Covalently with an Identical Protein or Proteins. 


     
  •   Gene Details   Hide

    Natural Source

    Chain M,N,O,P,Q,R
    Common Name Chicken
    Scientific Name Gallus gallus  
    Tissue Egg White

    Genetic Source

    Chain A,B,C,D,E,F,G,H,I,J,K,L
    Scientific Name Escherichia coli  
    Strain K-12
    Tissue Periplasm
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Pet26b
    Host Vector Type Plasmid


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    1 - 396218     lysozyme (renal amyloidosis) LYZ