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(-) Description

Title :  CRYSTAL STRUCTURE OF RAD50 ABC-ATPASE
 
Authors :  K. P. Hopfner, A. Karcher, D. S. Shin, L. Craig
Date :  29 May 00  (Deposition) - 02 Aug 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dna Double-Strand Break Repair, Abc-Atpase, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. P. Hopfner, A. Karcher, D. S. Shin, L. Craig, L. M. Arthur, J. P. Carney, J. A. Tainer
Structural Biology Of Rad50 Atpase: Atp-Driven Conformational Control In Dna Double-Strand Break Repair And The Abc-Atpase Superfamily.
Cell(Cambridge, Mass. ) V. 101 789 2000
PubMed-ID: 10892749  |  Reference-DOI: 10.1016/S0092-8674(00)80890-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAD50 ABC-ATPASE
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
 
Molecule 2 - RAD50 ABC-ATPASE
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:37 , GLN A:140 , ATP A:901 , HOH A:914 , HOH B:48BINDING SITE FOR RESIDUE MG A 902
2AC2SOFTWARESER C:37 , GLN C:140 , ATP C:901 , HOH C:919 , HOH D:50BINDING SITE FOR RESIDUE MG C 902
3AC3SOFTWAREARG A:12 , GLN A:31 , ASN A:32 , GLY A:33 , SER A:34 , GLY A:35 , LYS A:36 , SER A:37 , SER A:38 , GLU A:60 , THR A:62 , LYS A:63 , VAL A:64 , GLN A:140 , MG A:902 , HOH A:907 , HOH A:908 , HOH A:914 , HOH A:947 , HOH B:48 , HOH B:260 , GLU B:823 , HOH D:162 , LYS D:763 , TYR D:764 , PHE D:791 , SER D:793 , GLY D:794 , GLY D:795 , GLU D:796BINDING SITE FOR RESIDUE ATP A 901
4AC4SOFTWAREHOH B:12 , HOH B:283 , LYS B:763 , TYR B:764 , PHE B:791 , SER B:793 , GLY B:794 , GLY B:795 , GLU B:796 , ARG C:12 , SER C:13 , GLN C:31 , ASN C:32 , GLY C:33 , SER C:34 , GLY C:35 , LYS C:36 , SER C:37 , SER C:38 , GLU C:60 , THR C:62 , LYS C:63 , VAL C:64 , GLN C:140 , MG C:902 , HOH C:903 , HOH C:908 , HOH C:919 , HOH C:929 , HOH C:933 , HOH D:50 , GLU D:823BINDING SITE FOR RESIDUE ATP C 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F2U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:49 -Pro A:50
2Trp C:49 -Pro C:50

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F2U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F2U)

(-) Exons   (0, 0)

(no "Exon" information available for 1F2U)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:149
 aligned with RAD50_PYRFU | P58301 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
          RAD50_PYRFU     1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILES 149
               SCOP domains d1f2u.1 A:,B: Rad50                                                                                                                                   SCOP domains
               CATH domains 1f2uA00 A:1-149 P-loop containing nucleotide triphosphate hydrolases                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeeee...eeeeeee....hhhhhhhhhhhhhhh.......hhhhhh.....eeeeeeeeee..eeeeeeeeee.......eeeeeeee..eeee....hhhhhhhhhhhhhhhhhhhhhhee.....hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f2u A   1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILES 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         


Chain B from PDB  Type:PROTEIN  Length:145
 aligned with RAD50_PYRFU | P58301 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:145
                                   747       757       767       777       787       797       807       817       827       837       847       857       867       877     
          RAD50_PYRFU   738 ALAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 882
               SCOP domains d1f2u.1 A:,B: Rad50                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee....eeeeeee..eeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhh...eeeeeeee..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f2u B 738 ALAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 882
                                   747       757       767       777       787       797       807       817       827       837       847       857       867       877     


Chain C from PDB  Type:PROTEIN  Length:148
 aligned with RAD50_PYRFU | P58301 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
          RAD50_PYRFU     1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILE 148
               SCOP domains d1f2u.2 C:,D: Rad50                                                                                                                                  SCOP domains
               CATH domains 1f2uC00 C:1-148 P-loop containing nucleotide triphosphate hydrolases                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..eeeeeee...eeeeee.....hhhhhhhhhhhhhhh.......hhhhhh.....eeeeeeeeee..eeeeeeeeee..hhhhheeeeeeee..eeee....hhhhhhhhhhhhhhhhhhhhhhee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f2u C   1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILE 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        


Chain D from PDB  Type:PROTEIN  Length:142
 aligned with RAD50_PYRFU | P58301 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:142
                                   750       760       770       780       790       800       810       820       830       840       850       860       870       880  
          RAD50_PYRFU   741 REAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 882
               SCOP domains d1f2u.2 C:,D: Rad50                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.....eeeee......eeeeee..eeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhh.eeeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f2u D 741 REAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 882
                                   750       760       770       780       790       800       810       820       830       840       850       860       870       880
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F2U)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (RAD50_PYRFU | P58301)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0016787    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.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    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.
    GO:0005515    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).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006281    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.
    GO:0006974    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.
    GO:0006302    double-strand break repair    The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RAD50_PYRFU | P58301: 1f2t 1ii8 1l8d 1us8 3qkr 3qks 3qkt 3qku 4nch 4nci 4ncj 4nck

(-) Related Entries Specified in the PDB File

1f2t ATP FREE RAD50