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(-) Description

Title :  THE RAD50 SIGNATURE MOTIF: ESSENTIAL TO ATP BINDING AND BIOLOGICAL FUNCTION
 
Authors :  G. Moncalian, B. Lengsfeld, V. Bhaskara, K. P. Hopfner, A. Karcher, E. Alden, J. A. Tainer, T. T. Paull
Date :  20 Nov 03  (Deposition) - 25 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Repair, Abc Atpase, Signature Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Moncalian, B. Lengsfeld, V. Bhaskara, K. P. Hopfner, A. Karcher, E. Alden, J. A. Tainer, T. T. Paull
The Rad50 Signature Motif: Essential To Atp Binding And Biological Function
J. Mol. Biol. V. 335 937 2004
PubMed-ID: 14698290  |  Reference-DOI: 10.1016/J.JMB.2003.11.026

(-) Compounds

Molecule 1 - DNA DOUBLE-STRAND BREAK REPAIR RAD50 ATPASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: N-TERMINAL DOMAIN, RESIDUES 1-147
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: RAD50
 
Molecule 2 - DNA DOUBLE-STRAND BREAK REPAIR RAD50 ATPASE
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: C-TERMINAL DOMAIN, RESIDUES 739-882
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: RAD50

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1US8)

(-) Sites  (0, 0)

(no "Site" information available for 1US8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1US8)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1US8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1US8)

(-) Exons   (0, 0)

(no "Exon" information available for 1US8)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:129
 aligned with RAD50_PYRFU | P58301 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       
          RAD50_PYRFU     1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGYSSGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAIL 147
               SCOP domains d1us8.1 A:,B: Rad50                                                                                                                                 SCOP domains
               CATH domains 1us8A00 A:1-147 P-loop containing nucleotide triphosp              hate hydrolases                                                                  CATH domains
               Pfam domains ----AAA_23-1us8A01 A:5-147                                                                                                                          Pfam domains
         Sec.struct. author .eeeeeeee.......eeee...eeeeee.....hhhhhhhhhhhhhhh....--------------.eeeeeeeee..eeeeeeeee.----..eeeeeeeee..eeee....hhhhhhhhhhhhhhhhhhhhhheeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1us8 A   1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRI--------------DTYIDLIFEKDGTKYRITRRFL----SGEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAIL 147
                                    10        20        30        40        50  |      -       |70        80        |-   |   100       110       120       130       140       
                                                                               53             68                   89   94                                                     


Chain B from PDB  Type:PROTEIN  Length:140
 aligned with RAD50_PYRFU | P58301 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:144
                                   748       758       768       778       788       798       808       818       828       838       848       858       868       878    
          RAD50_PYRFU   739 LAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 882
               SCOP domains d1us8.1 A:,B: Rad50                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains AAA_21-1us8B01 B:739-861                                                                                                   --------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.....eeeee.----.eeeeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhh.eeeeeeee..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1us8 B 739 LAREAALSKIGELASEIFAEFTEGKYSEVVVRA----VRLFVVWEGKERPLTFLRGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERRRKLITIMERYLKKIPQVILVSHDEELKDAADHVIRISLENGSSKVEVVS 882
                                   748       758       768  |    778       788       798       808       818       828       838       848       858       868       878    
                                                          771  776
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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    Trp A:49 - Pro A:50   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAD50_PYRFU | P58301: 1f2t 1f2u 1ii8 1l8d 3qkr 3qks 3qkt 3qku 4nch 4nci 4ncj 4nck

(-) Related Entries Specified in the PDB File

1f2t CRYSTAL STRUCTURE OF ATP-FREE RAD50 ABC-ATPASE
1f2u CRYSTAL STRUCTURE OF RAD50 ABC-ATPASE
1ii8 CRYSTAL STRUCTURE OF THE P. FURIOSUS RAD50 ATPASE DOMAIN
1l8d RAD50 COILED-COIL ZN HOOK