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The structure of the Box CD enzyme reveals regulation of rRNA methylation
Biology and Chemistry Report
4BY9
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE/RNA
    Text TRANSFERASE-RNA COMPLEX, RRNA MODIFICATION

    Polymeric Molecules

    Chain A,B
    Description SSR26 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polyribonucleotide 
    Formula Weight 23525.2 
    Source Method synthetic  
    Chain C,F,I,L
    Description NOP5/NOP56 RELATED PROTEIN 
    Fragment RESIDUES 4-369 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 42303.0 
    Source Method genetically manipulated  
    Entity Name NOP5 
    Chain D,G,J,M
    Description 50S RIBOSOMAL PROTEIN L7AE 
    Fragment RESIDUES 3-123 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13212.5 
    Source Method genetically manipulated  
    Entity Name L7AE 
    Chain E,H,K,N
    Description FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 25801.0 
    Source Method genetically manipulated  
    Entity Name FIBRILLARIN 
    Chain W,X,Y,Z
    Description 5'-R(*UP*CP*GP*CP*CP*CP*AP*UP*CP*AP*CP)-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polyribonucleotide 
    Formula Weight 3402.1 
    Source Method synthetic  
    Entity Name SUBSTRATE RNA 

     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    C,F,I,L Q8U4M1_PYRFU Q8U4M1     
    D,G,J,M RL7A_PYRFU Q8U160     
    E,H,K,N FLPA_PYRFU Q8U4M2     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    E H K N  2.1.1      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain C,F,I,L
    GO ID   Ontology GO Term Definition
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 
    Chain D,G,J,M
    GO ID   Ontology GO Term Definition
    1682   TRNA 5' Leader Removal  Generation of the Mature 5' End of the TRNA Usually Via an Endonucleolytic Cleavage by Rnase P. 
    6364   RRNA Processing  Any Process Involved in the Conversion of a Primary Ribosomal RNA (rrna) Transcript Into One or More Mature RRNA Molecules. 
    6412   Translation  The Cellular Metabolic Process in Which a Protein Is Formed Using the Sequence of a Mature MRNA Molecule to Specify the Sequence of Amino Acids in a Polypeptide Chain. Translation Is Mediated by the Ribosome and Begins with the Formation of a Ternary Complex Between Aminoacylated Initiator Methionine TRNA GTP and Initiation Factor 2 Which Subsequently Associates with the Small Subunit of the Ribosome and an Mrna. Translation Ends with the Release of a Polypeptide Chain From the Ribosome. 
    8033   TRNA Processing  The Process in Which a Pre TRNA Molecule Is Converted to a Mature TRNA Ready For Addition of an Aminoacyl Group. 
    42254   Ribosome Biogenesis  A Cellular Process That Results in the Biosynthesis of Constituent Macromolecules Assembly and Arrangement of Constituent Parts of Ribosome Subunits; Includes Transport to the Sites of Protein Synthesis. 
    90501   RNA Phosphodiester Bond Hydrolysis  The RNA Metabolic Process in Which the Phosphodiester Bonds Between Ribonucleotides Are Cleaved by Hydrolysis. 
    90502   RNA Phosphodiester Bond Hydrolysis Endonucleolytic  The Chemical Reactions and Pathways Involving the Hydrolysis of Internal 3' 5' Phosphodiester Bonds in One or Two Strands of Ribonucleotides. 
    5622   Intracellular  The Living Contents of a Cell; the Matter Contained Within (but Not Including) the Plasma Membrane Usually Taken to Exclude Large Vacuoles and Masses of Secretory or Ingested Material. in Eukaryotes It Includes the Nucleus and Cytoplasm. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5840   Ribosome  An Intracellular Organelle About 200 a in Diameter Consisting of RNA and Protein. It Is the Site of Protein Biosynthesis Resulting From Translation of Messenger RNA (mrna). It Consists of Two Subunits One Large and One Small Each Containing Only Protein and Rna. Both the Ribosome and Its Subunits Are Characterized by Their Sedimentation Coefficients Expressed in Svedberg Units (symbol: S). Hence the Prokaryotic Ribosome (70s) Comprises a Large (50s) Subunit and a Small (30s) Subunit While the Eukaryotic Ribosome (80s) Comprises a Large (60s) Subunit and a Small (40s) Subunit. Two Sites On the Ribosomal Large Subunit Are Involved in Translation Namely the Aminoacyl Site (a Site) and Peptidyl Site (p Site). Ribosomes From Prokaryotes Eukaryotes Mitochondria and Chloroplasts Have Characteristically Distinct Ribosomal Proteins. 
    30529   Ribonucleoprotein Complex  A Macromolecular Complex Containing Both Protein and RNA Molecules. 
    3723   RNA Binding  Interacting Selectively and Non Covalently with an RNA Molecule or a Portion Thereof. 
    3735   Structural Constituent of Ribosome  The Action of a Molecule That Contributes to the Structural Integrity of the Ribosome. 
    4526   Ribonuclease P Activity  Catalysis of the Endonucleolytic Cleavage of RNA Removing 5' Extra Nucleotides From TRNA Precursor. 
    19843   RRNA Binding  Interacting Selectively and Non Covalently with Ribosomal Rna. 
    Chain E,H,K,N
    GO ID   Ontology GO Term Definition
    6364   RRNA Processing  Any Process Involved in the Conversion of a Primary Ribosomal RNA (rrna) Transcript Into One or More Mature RRNA Molecules. 
    8033   TRNA Processing  The Process in Which a Pre TRNA Molecule Is Converted to a Mature TRNA Ready For Addition of an Aminoacyl Group. 
    32259   Methylation  The Process in Which a Methyl Group Is Covalently Attached to a Molecule. 
    3723   RNA Binding  Interacting Selectively and Non Covalently with an RNA Molecule or a Portion Thereof. 
    8168   Methyltransferase Activity  Catalysis of the Transfer of a Methyl Group to an Acceptor Molecule. 
    16740   Transferase Activity  Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain C,F,I,L
    Scientific Name Pyrococcus furiosus  
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)


    Chain D,G,J,M
    Scientific Name Pyrococcus furiosus  
    Host Scientific Name Escherichia coli  
    Host Variant Rosetta 2
    Host Strain Bl21(de3)


    Chain E,H,K,N
    Scientific Name Pyrococcus furiosus  
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    - - 1467888     fibrillarin PF0059