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Ternary complex of Bloom's syndrome helicase
Biology and Chemistry Report
4O3M
  •   Structure Details   Hide

    Structure Keywords

    Keywords Hydrolase/DNA
    Text Winged Helix, Helicase, Hydrolase-DNA complex

    Polymeric Molecules

    Chain A
    Description Bloom syndrome protein 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 75002.9 
    Source Method genetically manipulated  
    Entity Name DNA helicase, RecQ-like type 2, RecQ2, RecQ protein-like 3 
    Chain P
    Description 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*AP*AP*G)-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 4932.3 
    Source Method synthetic  
    Chain T
    Description 5'-D(*CP*TP*TP*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*CP*TP*TP*A)-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 7247.7 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ADP  ADENOSINE-5'-DIPHOSPHATE  C10 H15 N5 O10 P2   427.20  View 
    CA  CALCIUM ION  Ca   40.08  View 
    EDO  1,2-ETHANEDIOL  C2 H6 O2   62.07  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A BLM_HUMAN P54132     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    3.6.4.12      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6260   DNA Replication  The Cellular Metabolic Process in Which a Cell Duplicates One or More Molecules of Dna. DNA Replication Begins When Specific Sequences Known As Origins of Replication Are Recognized and Bound by Initiation Proteins and Ends When the Original DNA Molecule Has Been Completely Duplicated and the Copies Topologically Separated. the Unit of Replication Usually Corresponds to the Genome of the Cell an Organelle or a Virus. the Template For Replication Can Either Be an Existing DNA Molecule or Rna. 
    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. 
    6310   DNA Recombination  Any Process in Which a New Genotype Is Formed by Reassortment of Genes Resulting in Gene Combinations Different From Those That Were Present in the Parents. in Eukaryotes Genetic Recombination Can Occur by Chromosome Assortment Intrachromosomal Recombination or Nonreciprocal Interchromosomal Recombination. Intrachromosomal Recombination Occurs by Crossing Over. in Bacteria It May Occur by Genetic Transformation Conjugation Transduction or F Duction. 
    44237   Cellular Metabolic Process  The Chemical Reactions and Pathways by Which Individual Cells Transform Chemical Substances. 
    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. 
    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. 
    3676   Nucleic Acid Binding  Interacting Selectively and Non Covalently with Any Nucleic Acid. 
    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. 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    8026   ATP Dependent Helicase Activity  Catalysis of the Reaction: ATP + H2o = Adp + Phosphate to Drive the Unwinding of a DNA or RNA Helix. 
    43140   ATP Dependent 3' 5' DNA Helicase Activity  Catalysis of the Reaction: ATP + H2o = Adp + Phosphate; Drives the Unwinding of the DNA Helix in the Direction 3' to 5'. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene blm, recq2, recql3
    Host Scientific Name Escherichia coli  
    Host Strain Rosetta 2 Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET15b


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    15 15q26.1 641     Bloom syndrome, RecQ helicase-like BLM    

    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
    rs201458487 LS-SNP   dbSNP   A 642 E - > K Coil 36% (Intermediate) 15 91306237
    rs201458487 LS-SNP   dbSNP   A 642 E - > K Coil 36% (Intermediate) 15 91306237
    rs12720097 LS-SNP   dbSNP   A 643 R - > H 3/10 Helix 67% (Exposed) 15 91306241
    rs12720097 LS-SNP   dbSNP   A 643 R - > H 3/10 Helix 67% (Exposed) 15 91306241
    rs187379039 LS-SNP   dbSNP   A 658 I - > T Helix 20% (Intermediate) 15 91306286
    rs187379039 LS-SNP   dbSNP   A 658 I - > T Helix 20% (Intermediate) 15 91306286
    rs139688226 LS-SNP   dbSNP   A 660 H - > Y Helix 49% (Exposed) 15 91306291
    rs139688226 LS-SNP   dbSNP   A 660 H - > Y Helix 49% (Exposed) 15 91306291
    rs146077918 LS-SNP   dbSNP   A 707 P - > S Bend 71% (Exposed) 15 91308570
    rs146077918 LS-SNP   dbSNP   A 707 P - > S Bend 71% (Exposed) 15 91308570
    rs28406486 LS-SNP   dbSNP   A 717 R - > T Helix 40% (Exposed) 15 91308601
    rs28406486 LS-SNP   dbSNP   A 717 R - > T Helix 40% (Exposed) 15 91308601
    rs61752785 LS-SNP   dbSNP   A 752 Q - > H Helix 23% (Intermediate) 15 91310202
    rs61752785 LS-SNP   dbSNP   A 752 Q - > H Helix 23% (Intermediate) 15 91310202
    rs142551229 LS-SNP   dbSNP   A 755 K - > E Bend 53% (Exposed) 15 91310209
    rs142551229 LS-SNP   dbSNP   A 755 K - > E Bend 53% (Exposed) 15 91310209
    rs191789336 LS-SNP   dbSNP   A 765 V - > I Beta Ladder 0% (Buried) 15 91310239
    rs191789336 LS-SNP   dbSNP   A 765 V - > I Beta Ladder 0% (Buried) 15 91310239
    rs139610577 LS-SNP   dbSNP   A 778 S - > C Helix 47% (Exposed) 15 91312388
    rs139610577 LS-SNP   dbSNP   A 778 S - > C Helix 47% (Exposed) 15 91312388
    rs149754073 LS-SNP   dbSNP   A 788 L - > FI Coil 21% (Intermediate) 15 91312417
    rs149754073 LS-SNP   dbSNP   A 788 L - > FI Coil 21% (Intermediate) 15 91312417
    rs55880859 LS-SNP   dbSNP   A 791 R - > C Beta Ladder 2% (Buried) 15 91312426
    rs55880859 LS-SNP   dbSNP   A 791 R - > C Beta Ladder 2% (Buried) 15 91312426
    rs148394770 LS-SNP   dbSNP   A 803 W - > R Coil 0% (Buried) 15 91312668
    rs148394770 LS-SNP   dbSNP   A 803 W - > R Coil 0% (Buried) 15 91312668
    rs145029382 LS-SNP   dbSNP   A 811 Y - > C Helix 19% (Intermediate) 15 91312693
    rs145029382 LS-SNP   dbSNP   A 811 Y - > C Helix 19% (Intermediate) 15 91312693
    rs201427280 LS-SNP   dbSNP   A 839 K - > E Helix 62% (Exposed) 15 91312776
    rs201427280 LS-SNP   dbSNP   A 839 K - > E Helix 62% (Exposed) 15 91312776
    rs137853152 LS-SNP   dbSNP   A 843 T - > I Helix 65% (Exposed) 15 91312789
    rs137853152 LS-SNP   dbSNP   A 843 T - > I Helix 65% (Exposed) 15 91312789
    rs11852361 LS-SNP   dbSNP   A 868 P - > L Beta Ladder 77% (Exposed) 15 91326099
    rs11852361 LS-SNP   dbSNP   A 868 P - > L Beta Ladder 77% (Exposed) 15 91326099
    rs146723808 LS-SNP   dbSNP   A 873 K - > N 3/10 Helix 16% (Intermediate) 15 91326115
    rs146723808 LS-SNP   dbSNP   A 873 K - > N 3/10 Helix 16% (Intermediate) 15 91326115
    rs201770808 LS-SNP   dbSNP   A 880 E - > Q Helix 31% (Intermediate) 15 91326134
    rs201770808 LS-SNP   dbSNP   A 880 E - > Q Helix 31% (Intermediate) 15 91326134
    rs151309611 LS-SNP   dbSNP   A 896 L - > F Bend 24% (Intermediate) 15 91328174
    rs151309611 LS-SNP   dbSNP   A 896 L - > F Bend 24% (Intermediate) 15 91328174
    rs201432297 LS-SNP   dbSNP   A 922 L - > P Bend 28% (Intermediate) 15 91328253
    rs201432297 LS-SNP   dbSNP   A 922 L - > P Bend 28% (Intermediate) 15 91328253
    rs189925962 LS-SNP   dbSNP   A 947 I - > V Turn 63% (Exposed) 15 91333894
    rs189925962 LS-SNP   dbSNP   A 947 I - > V Turn 63% (Exposed) 15 91333894
    rs150475674 LS-SNP   dbSNP   A 972 G - > V Helix 13% (Intermediate) 15 91333970
    rs150475674 LS-SNP   dbSNP   A 972 G - > V Helix 13% (Intermediate) 15 91333970
    rs138329850 LS-SNP   dbSNP   A 985 E - > D Bend 29% (Intermediate) 15 91334010
    rs138329850 LS-SNP   dbSNP   A 985 E - > D Bend 29% (Intermediate) 15 91334010
    rs142723411 LS-SNP   dbSNP   A 995 Y - > H Helix 9% (Intermediate) 15 91334038
    rs142723411 LS-SNP   dbSNP   A 995 Y - > H Helix 9% (Intermediate) 15 91334038
    rs201829983 LS-SNP   dbSNP   A 1005 I - > V Helix 3% (Buried) 15 91334068
    rs201829983 LS-SNP   dbSNP   A 1005 I - > V Helix 3% (Buried) 15 91334068
    rs145022945 LS-SNP   dbSNP   A 1014 H - > R Coil 54% (Exposed) 15 91337418
    rs145022945 LS-SNP   dbSNP   A 1014 H - > R Coil 54% (Exposed) 15 91337418
    rs202196488 LS-SNP   dbSNP   A 1015 T - > I Helix 45% (Exposed) 15 91337421
    rs202196488 LS-SNP   dbSNP   A 1015 T - > I Helix 45% (Exposed) 15 91337421
    rs201676342 LS-SNP   dbSNP   A 1024 Y - > C Helix 19% (Intermediate) 15 91337448
    rs201676342 LS-SNP   dbSNP   A 1024 Y - > C Helix 19% (Intermediate) 15 91337448
    rs137853153 LS-SNP   dbSNP   A 1036 C - > F Coil 8% (Buried) 15 91337484 NULL
    rs137853153 LS-SNP   dbSNP   A 1036 C - > F Coil 8% (Buried) 15 91337484 NULL
    rs2229035 LS-SNP   dbSNP   A 1043 A - > D Helix 42% (Exposed) 15 91337505
    rs2229035 LS-SNP   dbSNP   A 1043 A - > D Helix 42% (Exposed) 15 91337505
    rs144021705 LS-SNP   dbSNP   A 1074 T - > I Coil 76% (Exposed) 15 91341430
    rs144021705 LS-SNP   dbSNP   A 1074 T - > I Coil 76% (Exposed) 15 91341430
    rs150784889 LS-SNP   dbSNP   A 1104 G - > D Coil 0% (Buried) 15 91341520
    rs141269464 LS-SNP   dbSNP   A 1104 G - > S Coil 0% (Buried) 15 91341519
    rs150784889 LS-SNP   dbSNP   A 1104 G - > D Coil 0% (Buried) 15 91341520
    rs141269464 LS-SNP   dbSNP   A 1104 G - > S Coil 0% (Buried) 15 91341519
    rs200993043 LS-SNP   dbSNP   A 1105 P - > L Coil 48% (Exposed) 15 91341523
    rs200993043 LS-SNP   dbSNP   A 1105 P - > L Coil 48% (Exposed) 15 91341523
    rs139773499 LS-SNP   dbSNP   A 1120 G - > R Turn 32% (Intermediate) 15 91341567
    rs139773499 LS-SNP   dbSNP   A 1120 G - > R Turn 32% (Intermediate) 15 91341567
    rs145027663 LS-SNP   dbSNP   A 1133 K - > E Turn 45% (Exposed) 15 91346789
    rs145027663 LS-SNP   dbSNP   A 1133 K - > E Turn 45% (Exposed) 15 91346789
    rs140387675 LS-SNP   dbSNP   A 1143 E - > K Helix 29% (Intermediate) 15 91346819
    rs140387675 LS-SNP   dbSNP   A 1143 E - > K Helix 29% (Intermediate) 15 91346819
    rs142928725 LS-SNP   dbSNP   A 1198 V - > M Coil 0% (Buried) 15 91347430
    rs142928725 LS-SNP   dbSNP   A 1198 V - > M Coil 0% (Buried) 15 91347430
    rs28385141 LS-SNP   dbSNP   A 1205 V - > I Coil 0% (Buried) 15 91347451
    rs28385141 LS-SNP   dbSNP   A 1205 V - > I Coil 0% (Buried) 15 91347451
    rs1801256 LS-SNP   dbSNP   A 1209 S - > T Coil 50% (Exposed) 15 91347463
    rs1801256 LS-SNP   dbSNP   A 1209 S - > T Coil 50% (Exposed) 15 91347463
    rs28385142 LS-SNP   dbSNP   A 1213 E - > K Helix 59% (Exposed) 15 91347475
    rs28385142 LS-SNP   dbSNP   A 1213 E - > K Helix 59% (Exposed) 15 91347475
    rs144964365 LS-SNP   dbSNP   A 1257 P - > A Helix 42% (Exposed) 15 91352384
    rs144964365 LS-SNP   dbSNP   A 1257 P - > A Helix 42% (Exposed) 15 91352384