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(-) Description

Title :  RAD50 COILED-COIL ZN HOOK
 
Authors :  K. P. Hopfner, J. A. Tainer
Date :  20 Mar 02  (Deposition) - 28 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Zinc Finger, Rad50, Dna Repair, Recombination, Hook Motif, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. P. Hopfner, L. Craig, G. Moncalian, R. A. Zinkel, T. Usui, B. A. Owen, A. Karcher, B. Henderson, J. L. Bodmer, C. T. Mcmurray, J. P. Carney, J. H. Petrini, J. A. Tainer
The Rad50 Zinc-Hook Is A Structure Joining Mre11 Complexes In Dna Recombination And Repair.
Nature V. 418 562 2002
PubMed-ID: 12152085  |  Reference-DOI: 10.1038/NATURE00922
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA DOUBLE-STRAND BREAK REPAIR RAD50 ATPASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RAD50 COILED-COIL FRAGMENT CONTAINING THE CXXC MOTIF, RAD50 MOLECULAR HOOK
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2HG1Ligand/IonMERCURY (II) ION
3PO46Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:444 , CYS A:447 , CYS B:444 , CYS B:447BINDING SITE FOR RESIDUE HG A 201
2AC2SOFTWAREARG B:449BINDING SITE FOR RESIDUE PO4 B 301
3AC3SOFTWARECIT A:507BINDING SITE FOR RESIDUE PO4 A 302
4AC4SOFTWAREHOH A:82 , HOH A:109 , LYS A:441 , ASP A:453 , ARG A:456BINDING SITE FOR RESIDUE PO4 A 303
5AC5SOFTWAREARG A:456 , GLU A:457 , LEU A:460BINDING SITE FOR RESIDUE PO4 A 304
6AC6SOFTWARELYS A:431 , THR A:432 , GLU A:435BINDING SITE FOR RESIDUE PO4 A 305
7AC7SOFTWAREGLU A:403 , ARG B:413 , LYS B:481 , GLU B:485BINDING SITE FOR RESIDUE PO4 A 306
8AC8SOFTWAREHOH A:69 , PO4 A:302 , LYS A:406 , GLU A:410 , ARG A:413 , LEU A:488 , GLU B:403 , LYS B:406 , ILE B:495BINDING SITE FOR RESIDUE CIT A 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L8D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1L8D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L8D)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZN_HOOKPS51131 Rad50 zinc-hook domain profile.RAD50_PYRFU399-496
 		  2A:399-496
B:399-496

(-) Exons   (0, 0)

(no "Exon" information available for 1L8D)

(-) 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:103
 aligned with RAD50_PYRFU | P58301 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:103
                                   405       415       425       435       445       455       465       475       485       495   
          RAD50_PYRFU   396 KKLLEELETKKTTIEEERNEITQRIGELKNKIGDLKTAIEELKKAKGKCPVCGRELTDEHREELLSKYHLDLNNSKNTLAKLIDRKSELERELRRIDMEIKRL 498
               SCOP domains d1l8da_ A: Rad50 coiled-coil Zn hook                                                                    SCOP domains
               CATH domains 1l8dA00 A:396-498 Helix hairpin bin                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ZN_HOOK  PDB: A:399-496 UniProt: 399-496                                                          -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1l8d A 396 KKLLEELETKKTTIEEERNEITQRIGELKNKIGDLKTAIEELKKAKGKCPVCGRELTDEHREELLSKYHLDLNNSKNTLAKLIDRKSELERELRRIDMEIKRL 498
                                   405       415       425       435       445       455       465       475       485       495   


Chain B from PDB  Type:PROTEIN  Length:102
 aligned with RAD50_PYRFU | P58301 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:102
                                   404       414       424       434       444       454       464       474       484       494  
          RAD50_PYRFU   395 IKKLLEELETKKTTIEEERNEITQRIGELKNKIGDLKTAIEELKKAKGKCPVCGRELTDEHREELLSKYHLDLNNSKNTLAKLIDRKSELERELRRIDMEIK 496
               SCOP domains d1l8db_ B: Rad50 coiled-coil Zn hook                                                                   SCOP domains
               CATH domains 1l8dB00 B:395-496 Helix hairpin bin                                                                    CATH domains
           Pfam domains (1) ---------------------------Rad50_zn_hook-1l8dB01 B:422-475                       --------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------Rad50_zn_hook-1l8dB02 B:422-475                       --------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----ZN_HOOK  PDB: B:399-496 UniProt: 399-496                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1l8d B 395 MKKLLEELETKKTTIEEERNEITQRIGELKNKIGDLKTAIEELKKAKGKCPVCGRELTDEHREELLSKYHLDLNNSKNTLAKLIDRKSELERELRRIDMEIK 496
                                   404       414       424       434       444       454       464       474       484       494
   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: Coiled coil proteins (689)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Rad50_zn_hook] (1)

(-) 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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  1l8d
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  RAD50_PYRFU | P58301
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 Related Entries

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

UniProtKB/Swiss-Prot
        RAD50_PYRFU | P58301: 1f2t 1f2u 1ii8 1us8 3qkr 3qks 3qkt 3qku 4nch 4nci 4ncj 4nck

(-) Related Entries Specified in the PDB File

1f2t RAD50 ATPASE DOMAIN
1f2u RAD50 ATPASE DOMAIN+ATP
1ii7 MRE11
1ii8 RAD50 ATPASE DOMAIN+COILED-COIL