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Crystal structure of ADPNP-bound AddAB with a forked DNA substrate
Biology and Chemistry Report
4CEI
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/DNA
    Text HYDROLASE-DNA COMPLEX, HELICASE-NUCLEASE, BACTERIAL PROTEINS, BINDING SITES, DNA BREAKS, DOUBLE-STRANDED, DNA HELICASES, DNA REPAIR, SINGLE-STRANDED, DNA- BINDING PROTEINS, DEOXYRIBONUCLEASES, EXODEOXYRIBONUCLEASE V, EXODEOXYRIBONUCLEASES, HOMOLOGOUS RECOMBINATION

    Polymeric Molecules

    Chain A
    Description ATP-DEPENDENT HELICASE/NUCLEASE SUBUNIT A 
    Mutation YES 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 141220.0 
    Source Method genetically manipulated  
    Entity Name ATP-DEPENDENT HELICAS E-NUCLEASE SUBUNIT A 
    Chain B
    Description ATP-DEPENDENT HELICASE/DEOXYRIBONUCLEASE SUBUNIT B 
    Mutation YES 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 134770.0 
    Source Method genetically manipulated  
    Entity Name ATP-DEPENDENT HELICAS E-NUCLEASE SUBUNIT B 
    Chain X
    Description DNA 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 19956.9 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ANP  PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER  C10 H17 N6 O12 P3   506.20  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    SF4  IRON/SULFUR CLUSTER  Fe4 S4   351.64  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A ADDA_BACSU P23478     
    B ADDB_BACSU P23477     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    3.1      
    3.6.4.12      
    3.1      
    3.6.4.12      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6281   DNA Repair  The Process of Restoring DNA After Damage. Genomes Are Subject to Damage by Chemical and Physical Agents in the Environment (e.g. Uv and Ionizing Radiations Chemical Mutagens Fungal and Bacterial Toxins Etc.) and by Free Radicals or Alkylating Agents Endogenously Generated in Metabolism. DNA Is Also Damaged Because of Errors During Its Replication. a Variety of Different DNA Repair Pathways Have Been Reported That Include Direct Reversal Base Excision Repair Nucleotide Excision Repair Photoreactivation Bypass Double Strand Break Repair Pathway and Mismatch Repair Pathway. 
    6974   Cellular Response to DNA Damage Stimulus  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Stimulus Indicating Damage to Its DNA From Environmental Insults or Errors During Metabolism. 
    90305   Nucleic Acid Phosphodiester Bond Hydrolysis  The Nucleic Acid Metabolic Process in Which the Phosphodiester Bonds Between Nucleotides Are Cleaved by Hydrolysis. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    4386   Helicase Activity  Catalysis of the Reaction: Ntp + H2o = Ndp + Phosphate to Drive the Unwinding of a DNA or RNA Helix. 
    4518   Nuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Nucleic Acids. 
    4527   Exonuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Nucleic Acids by Removing Nucleotide Residues From the 3' or 5' End. 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    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. 
    Chain B
    GO ID   Ontology GO Term Definition
    6281   DNA Repair  The Process of Restoring DNA After Damage. Genomes Are Subject to Damage by Chemical and Physical Agents in the Environment (e.g. Uv and Ionizing Radiations Chemical Mutagens Fungal and Bacterial Toxins Etc.) and by Free Radicals or Alkylating Agents Endogenously Generated in Metabolism. DNA Is Also Damaged Because of Errors During Its Replication. a Variety of Different DNA Repair Pathways Have Been Reported That Include Direct Reversal Base Excision Repair Nucleotide Excision Repair Photoreactivation Bypass Double Strand Break Repair Pathway and Mismatch Repair Pathway. 
    6974   Cellular Response to DNA Damage Stimulus  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Stimulus Indicating Damage to Its DNA From Environmental Insults or Errors During Metabolism. 
    90305   Nucleic Acid Phosphodiester Bond Hydrolysis  The Nucleic Acid Metabolic Process in Which the Phosphodiester Bonds Between Nucleotides Are Cleaved by Hydrolysis. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    4518   Nuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Nucleic Acids. 
    4527   Exonuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Nucleic Acids by Removing Nucleotide Residues From the 3' or 5' End. 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    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. 
    51536   Iron Sulfur Cluster Binding  Interacting Selectively and Non Covalently with an Iron Sulfur Cluster a Combination of Iron and Sulfur Atoms. 
    51539   4 Iron 4 Sulfur Cluster Binding  Interacting Selectively and Non Covalently with a 4 Iron 4 Sulfur (4fe 4s) Cluster; This Cluster Consists of Four Iron Atoms with the Inorganic Sulfur Atoms Found Between the Irons and Acting As Bridging Ligands. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B
    Scientific Name Bacillus subtilis subsp. subtilis str. 168  
    ATCC Source 23857
    Host Scientific Name Escherichia coli b  
    Host Strain B834 (de3)
    Host Vector Type Plasmid
    Host Plasmid Name PCOLADUET-1


    Chain A
    Scientific Name Bacillus subtilis subsp. subtilis str. 168  
    ATCC Source 23857
    Host Scientific Name Escherichia coli b  
    Host Strain B834 (de3)
    Host Vector Type Plasmid
    Host Plasmid Name PCOLADUET-1


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    - - 939793     ATP-dependent helicase/nuclease subunit A ADDA    
    - - 936341     ATP-dependent helicase/deoxyribonuclease subunit B ADDB