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(-) Description

Title :  CRYSTAL STRUCTURE OF P. FURIOSUS MRE11-H85S BOUND TO A BRANCHED DNA AND MANGANESE
 
Authors :  R. S. Williams, D. Moiani, J. A. Tainer
Date :  11 Jul 08  (Deposition) - 14 Oct 08  (Release) - 28 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Dna Complex, Double Helix, Nuclease, Dna Damage, Dna Repair, Endonuclease, Exonuclease, Hydrolase, Manganese, Metal-Binding, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. S. Williams, G. Moncalian, J. S. Williams, Y. Yamada, O. Limbo, D. S. Shin, L. M. Groocock, D. Cahill, C. Hitomi, G. Guenther, D. Moiani, J. P. Carney, P. Russell, J. A. Tainer
Mre11 Dimers Coordinate Dna End Bridging And Nuclease Processing In Double-Strand-Break Repair.
Cell(Cambridge, Mass. ) V. 135 97 2008
PubMed-ID: 18854158  |  Reference-DOI: 10.1016/J.CELL.2008.08.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PFMRE11 NUCLEASE DOMAIN
    Gene: MRE11, PF1166
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: PFMRE11
 
Molecule 2 - DNA (5'- D(*DCP*DGP*DCP*DGP*DCP*DAP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DTP* DTP*DGP*DCP*DTP*DTP*DGP*DTP*DGP*DGP*DAP*DTP*DA)-3')
    Chains: C
    Engineered: YES
    Fragment: BRANCHED DNA HAIRPIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , HIS A:10 , ASP A:49 , HIS A:208 , MN A:404BINDING SITE FOR RESIDUE MN A 403
2AC2SOFTWAREASP A:8 , ASP A:49 , ASN A:84 , HIS A:173 , HIS A:206 , MN A:403BINDING SITE FOR RESIDUE MN A 404
3AC3SOFTWAREASP B:49 , ASN B:84 , HIS B:173 , HIS B:206 , MN B:406BINDING SITE FOR RESIDUE MN B 405
4AC4SOFTWAREASP B:8 , HIS B:10 , ASP B:49 , HIS B:208 , MN B:405BINDING SITE FOR RESIDUE MN B 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DSD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DSD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DSD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DSD)

(-) Exons   (0, 0)

(no "Exon" information available for 3DSD)

(-) 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:333
 aligned with MRE11_PYRFU | Q8U1N9 from UniProtKB/Swiss-Prot  Length:426

    Alignment length:333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   
          MRE11_PYRFU     1 MKFAHLADIHLGYEQFHKPQREEEFAEAFKNALEIAVQENVDFILIAGDLFHSSRPSPGTLKKAIALLQIPKEHSIPVFAIEGNHDRTQRGPSVLNLLEDFGLVYVIGMRKEKVENEYLTSERLGNGEYLVKGVYKDLEIHGMKYMSSAWFEANKEILKRLFRPTDNAILMLHQGVREVSEARGEDYFEIGLGDLPEGYLYYALGHIHKRYETSYSGSPVVYPGSLERWDFGDYEVRYEWDGIKFKERYGVNKGFYIVEDFKPRFVEIKVRPFIDVKIKGSEEEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNVEYLKIDTWRI 333
               SCOP domains d3dsda_ A: Mre11                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3dsdA01 A:1-228,A:251-271  [code=3.60.21.10, no name defined]                                                                                                                                                                       ----------------------3dsdA01              -------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh...eeee...........hhhhhhhhh...ee.eee........eeeee.....eeeeeee..eeeeee...hhhhhhhh.hhhhhhh.....eeeeee..hhhhhhh........hhhhh.....eeeee.....eeeee..eeeee.......hhhhh.eeeee....eeeee....eeeeee..eeeeee.....eeeeeeeehhhhhhhhhhhhhhhh....eeeeeeee.....hhhhhhhh...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dsd A   1 MKFAHLADIHLGYEQFHKPQREEEFAEAFKNALEIAVQENVDFILIAGDLFHSSRPSPGTLKKAIALLQIPKEHSIPVFAIEGNSDRTQRGPSVLNLLEDFGLVYVIGMRKEKVENEYLTSERLGNGEYLVKGVYKDLEIHGMKYMSSAWFEANKEILKRLFRPTDNAILMLHQGVREVSEARGEDYFEIGLGDLPEGYLYYALGHIHKRYETSYSGSPVVYPGSLERWDFGDYEVRYEWDGIKFKERYGVNKGFYIVEDFKPRFVEIKVRPFIDVKIKGSEEEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNVEYLKIDTWRI 333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   


Chain B from PDB  Type:PROTEIN  Length:333
 aligned with MRE11_PYRFU | Q8U1N9 from UniProtKB/Swiss-Prot  Length:426

    Alignment length:333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   
          MRE11_PYRFU     1 MKFAHLADIHLGYEQFHKPQREEEFAEAFKNALEIAVQENVDFILIAGDLFHSSRPSPGTLKKAIALLQIPKEHSIPVFAIEGNHDRTQRGPSVLNLLEDFGLVYVIGMRKEKVENEYLTSERLGNGEYLVKGVYKDLEIHGMKYMSSAWFEANKEILKRLFRPTDNAILMLHQGVREVSEARGEDYFEIGLGDLPEGYLYYALGHIHKRYETSYSGSPVVYPGSLERWDFGDYEVRYEWDGIKFKERYGVNKGFYIVEDFKPRFVEIKVRPFIDVKIKGSEEEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNVEYLKIDTWRI 333
               SCOP domains d3dsdb_ B: Mre11                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3dsdB01 B:1-228,B:251-271  [code=3.60.21.10, no name defined]                                                                                                                                                                       ----------------------3dsdB01              -------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh...eeee...........hhhhhhhhh...ee.eee........eeeee.....eeeeeee..eeeeee...hhhhhhhh.hhhhhhh.....eeeee...hhhhhhhh.......hhhhh.....eee.......eeeee..eeeee.......hhhhh.eeeee....eeeee....eeeeee..eeeeee.....eeeeeeeehhhhhhhhhhhhhhhh....eeeeeeee.....hhhhhhhhh..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dsd B   1 MKFAHLADIHLGYEQFHKPQREEEFAEAFKNALEIAVQENVDFILIAGDLFHSSRPSPGTLKKAIALLQIPKEHSIPVFAIEGNSDRTQRGPSVLNLLEDFGLVYVIGMRKEKVENEYLTSERLGNGEYLVKGVYKDLEIHGMKYMSSAWFEANKEILKRLFRPTDNAILMLHQGVREVSEARGEDYFEIGLGDLPEGYLYYALGHIHKRYETSYSGSPVVYPGSLERWDFGDYEVRYEWDGIKFKERYGVNKGFYIVEDFKPRFVEIKVRPFIDVKIKGSEEEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNVEYLKIDTWRI 333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   


Chain C from PDB  Type:DNA  Length:23
                                                       
                 3dsd C   4 GCACAAGCTTTTGCTTGTGGATA  26
                                    13        23
   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) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DSD)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MRE11_PYRFU | Q8U1N9)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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).
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.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MRE11_PYRFU | Q8U1N9: 1ii7 1s8e 3dsc 3qkr 3qks 3qku 4hd0

(-) Related Entries Specified in the PDB File

1ii7 1s8e 3dsc