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Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 mutant (E336A) in complex with a synthetic CSIM tetrapeptide from the C-terminus of prelamin A
Biology and Chemistry Report
2YPT
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/PEPTIDE
    Text HYDROLASE-PEPTIDE COMPLEX, M48 PEPTIDASE, INTEGRAL MEMBRANE PROTEIN, PRELAMIN A PROCESSING, AGEING, PROGERIA

    Polymeric Molecules

    Chain A,B,D,E
    Description CAAX PRENYL PROTEASE 1 HOMOLOG 
    Mutation YES 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 55649.1 
    Source Method genetically manipulated  
    Entity Name FARNESYLATED PROTEINS-CONVERTING ENZYME 1, FACE-1, PRENYL PROTEIN-SPECIFIC ENDOPROTEASE 1, ZINC METALLOPROTEINASE STE24 HOMOLOG 
    Chain F,G,H,I
    Description PRELAMIN-A/C 
    Fragment C-TERMINAL TETRAPEPTIDE, RESIDUES 661-664 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 452.6 
    Source Method synthetic  
    Entity Name 70 KDA LAMIN, RENAL CARCINOMA ANTIGEN NY-REN-32, PRELAMIN A 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,D,E FACE1_HUMAN B3KQI7     
    F,G,H,I LMNA_HUMAN B4DI32     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B D E  3.4.24.84      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,D,E
    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. 
    6998   Nuclear Envelope Organization  A Process That Is Carried Out At the Cellular Level Which Results in the Assembly Arrangement of Constituent Parts or Disassembly of the Nuclear Envelope. 
    30327   Prenylated Protein Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Prenylated Proteins. 
    71586   Caax Box Protein Processing  The Second Process in a Series of Specific Posttranslational Modifications to the Caax Box Region of Caax Box Proteins in Which the Last Three Amino Acids of the Protein (aax) Are Removed by Proteolysis. 
    5634   Nucleus  A Membrane Bounded Organelle of Eukaryotic Cells in Which Chromosomes Are Housed and Replicated. in Most Cells the Nucleus Contains All of the Cell's Chromosomes Except the Organellar Chromosomes and Is the Site of RNA Synthesis and Processing. in Some Species or in Specialized Cell Types RNA Metabolism or DNA Replication May Be Absent. 
    5637   Nuclear Inner Membrane  The Inner I.e. Lumen Facing Lipid Bilayer of the Nuclear Envelope. 
    5783   Endoplasmic Reticulum  The Irregular Network of Unit Membranes Visible Only by Electron Microscopy That Occurs in the Cytoplasm of Many Eukaryotic Cells. the Membranes Form a Complex Meshwork of Tubular Channels Which Are Often Expanded Into Slitlike Cavities Called Cisternae. the Er Takes Two Forms Rough (or Granular) with Ribosomes Adhering to the Outer Surface and Smooth (with No Ribosomes Attached). 
    5789   Endoplasmic Reticulum Membrane  The Lipid Bilayer Surrounding the Endoplasmic Reticulum. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    16021   Integral Component of Membrane  The Component of a Membrane Consisting of Gene Products and Protein Complexes That Have Some Part That Penetrates At Least One Leaflet of the Membrane Bilayer. This Component Includes Gene Products That Are Buried in the Bilayer with No Exposure Outside the Bilayer. 
    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. 
    4222   Metalloendopeptidase Activity  Catalysis of the Hydrolysis of Internal Alpha Peptide Bonds in a Polypeptide Chain by a Mechanism in Which Water Acts As a Nucleophile One or Two Metal Ions Hold the Water Molecule in Place and Charged Amino Acid Side Chains Are Ligands For the Metal Ions. 
    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. 
    8235   Metalloexopeptidase Activity  Catalysis of the Hydrolysis of a Peptide Bond Not More Than Three Residues From the N or C Terminus of a Polypeptide Chain by a Mechanism in Which Water Acts As a Nucleophile One or Two Metal Ions Hold the Water Molecule in Place and Charged Amino Acid Side Chains Are Ligands For the Metal Ions. 
    8237   Metallopeptidase Activity  Catalysis of the Hydrolysis of Peptide Bonds by a Mechanism in Which Water Acts As a Nucleophile One or Two Metal Ions Hold the Water Molecule in Place and Charged Amino Acid Side Chains Are Ligands For the Metal Ions. 
    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. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B,D,E
    Common Name Human
    Scientific Name Homo sapiens  
    Host Common Name Fall Armyworm
    Host Scientific Name Spodoptera frugiperda  
    Host Cell Line Sf9
    Host Vector Type Baculovirus
    Host Plasmid Name PFB-CT10HF-LIC


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    1 1p34 10269     zinc metallopeptidase STE24 ZMPSTE24    
    1 1q22 4000     lamin A/C LMNA    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs1046247 LS-SNP   dbSNP   A 16 E - > K Helix 15% (Intermediate) 1 40723989
    rs114340421 LS-SNP   dbSNP   A 29 T - > I Helix 51% (Exposed) 1 40724029
    rs199508639 LS-SNP   dbSNP   A 53 P - > L Bend 72% (Exposed) 1 40726545
    rs199582862 LS-SNP   dbSNP   A 71 Q - > E Helix 13% (Intermediate) 1 40726598
    rs17853725 LS-SNP   dbSNP   A 137 T - > A Helix 19% (Intermediate) 1 40734142
    rs112521665 LS-SNP   dbSNP   A 142 S - > G Helix 42% (Exposed) 1 40734157
    rs145639744 LS-SNP   dbSNP   A 181 V - > M Helix 33% (Intermediate) 1 40735713
    rs199984135 LS-SNP   dbSNP   A 198 I - > F Helix 40% (Exposed) 1 40735764
    rs202090930 LS-SNP   dbSNP   A 203 F - > L Helix 20% (Intermediate) 1 40735781
    rs121908095 LS-SNP   dbSNP   A 248 P - > L Coil 57% (Exposed) 1 40737681
    rs200695349 LS-SNP   dbSNP   A 277 I - > V Beta Ladder 12% (Intermediate) 1 40747074
    rs28581527 LS-SNP   dbSNP   A 322 Q - > R Coil 56% (Exposed) 1 40751607
    rs121908093 LS-SNP   dbSNP   A 340 W - > R Helix 40% (Exposed) 1 40751660
    rs41268053 LS-SNP   dbSNP   A 369 R - > Q Coil 16% (Intermediate) 1 40756572
    rs200751802 LS-SNP   dbSNP   A 420 A - > G Helix 55% (Exposed) 1 40758172
    rs116771294 LS-SNP   dbSNP   A 438 L - > F Helix 9% (Buried) 1 40758225
    rs11577203 LS-SNP   dbSNP   A 451 L - > V Helix 29% (Intermediate) 1 40758264
    rs146105624 LS-SNP   dbSNP   A 462 L - > V Helix 15% (Intermediate) 1 40758297