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(-) Description

Title :  CRYSTAL STRUCTURE OF MRE11-RAD50 BOUND TO ATP S
 
Authors :  H. S. Lim, J. S. Kim, Y. Cho
Date :  18 Feb 11  (Deposition) - 25 May 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Repair, Calcineurin-Like Phosphoesterase, Abc Transporter Atpase Domain-Like, Dna Double-Strand Break Repair, Hera-Nura Complex, Nbs1 In Eukaryotes, Recombination (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. S. Lim, J. S. Kim, Y. B. Park, G. H. Gwon, Y. Cho
Crystal Structure Of The Mre11-Rad50-Atp S Complex: Understanding The Interplay Between Mre11 And Rad50
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NUCLEASE DOMAIN (UNP RESIDUES 1-313)
    Gene: RAD50, MJ1322
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
 
Molecule 2 - DNA DOUBLE-STRAND BREAK REPAIR RAD50 ATPASE
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: ABC ATPASE DOMAIN (UNP RESIDUES 1-190, 825-1005)
    Gene: RAD50, MJ1322
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII, METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190, 2190
    Other Details: THE FUSION PROTEIN OF RESIDUES 1-190 AND RESIDUES 825- 1005
    Synonym: RAD50 ABC-ATPASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1AGS1Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
2GOL4Ligand/IonGLYCEROL
3IPA3Ligand/IonISOPROPYL ALCOHOL
4MG1Ligand/IonMAGNESIUM ION
5SO41Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:30 , LYS A:59 , ARG A:62 , HOH A:701BINDING SITE FOR RESIDUE GOL A 500
02AC2SOFTWAREASP A:108 , TYR A:126 , GLU A:135 , LYS A:139BINDING SITE FOR RESIDUE IPA A 600
03AC3SOFTWAREARG A:211 , SO4 A:400 , GLU B:885 , ASP B:887BINDING SITE FOR RESIDUE IPA B 601
04AC4SOFTWAREGLN A:15 , TYR A:16 , TYR A:210 , ARG A:211 , IPA B:601BINDING SITE FOR RESIDUE SO4 A 400
05AC5SOFTWARELYS B:14 , SER B:15 , ASN B:34 , GLY B:35 , SER B:36 , GLY B:37 , LYS B:38 , SER B:39 , SER B:40 , THR B:60 , ILE B:62 , THR B:63 , LYS B:64 , GLN B:134 , TYR B:890 , LEU B:910 , ASN B:914 , SER B:916 , GLY B:917 , GLY B:918 , GLU B:919 , GLU B:947 , LYS B:994 , MG B:1007 , HOH B:1400BINDING SITE FOR RESIDUE AGS B 1006
06AC6SOFTWARESER B:39 , GLN B:134 , AGS B:1006 , HOH B:1400 , HOH B:1401BINDING SITE FOR RESIDUE MG B 1007
07AC7SOFTWAREGLY B:135 , TYR B:951BINDING SITE FOR RESIDUE GOL B 1200
08AC8SOFTWARETHR B:949 , VAL B:950 , TYR B:951 , HIS B:978 , HIS B:979BINDING SITE FOR RESIDUE GOL B 1201
09AC9SOFTWAREASP B:59 , LYS B:64 , GLY B:65 , LYS B:66 , HOH B:1404 , HOH B:1408BINDING SITE FOR RESIDUE GOL B 1202
10BC1SOFTWAREGLN B:134 , GLY B:917 , GLN B:920 , TYR B:951BINDING SITE FOR RESIDUE IPA B 1300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AV0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3AV0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AV0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AV0)

(-) Exons   (0, 0)

(no "Exon" information available for 3AV0)

(-) 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:369
 aligned with MRE11_METJA | Q58719 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:369
                               1                                                                                                                                                                                                                                                                                                                                                                             
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357         
         MRE11_METJA      - ---MMFVHIADNHLGYRQYNLDDREKDIYDSFKLCIKKILEIKPDVVLHSGDLFNDLRPPVKALRIAMQAFKKLHENNIKVYIVAGNHEMPRRLGEESPLALLKDYVKILDGKDVINVNGEEIFICGTYYHKKSKREEMLDKLKNFESEAKNYKKKILMLHQGINPYIPLDYELEHFDLPKFSYYALGHIHKRILERFNDGILAYSGSTEIIYRNEYEDYKKEGKGFYLVDFSGNDLDISDIEKIDIECREFVEVNIKDKKSFNEAVNKIERCKNKPVVFGKIKREFKPWFDTLKDKILINKAIIVDDEFIDMPDNVDIESLNIKELLVDYANRQGIDGDLVLSLYKALLNNENWKELLDEYYNTKFRG  366
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhhhh..eeee..hhhhh.......hhhhhhh...ee..eeeeeee..eeeeeeee......hhhhhhhhhhhhhhhhhh...eeeee..............hhhhh....eeee......eeee....eeee.......hhhhhhhhhhhh.eeeeee......hhh.eeeee.....eeeeee.hhhhhhhhhhhhh......eeeeeee.hhh..hhhhh....eeeeeee................hhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3av0 A   -2 GSHMMFVHIADNHLGYRQYNLDDREKDIYDSFKLCIKKILEIKPDVVLHSGDLFNDLRPPVKALRIAMQAFKKLHENNIKVYIVAGNHEMPRRLGEESPLALLKDYVKILDGKDVINVNGEEIFICGTYYHKKSKREEMLDKLKNFESEAKNYKKKILMLHQGINPYIPLDYELEHFDLPKFSYYALGHIHKRILERFNDGILAYSGSTEIIYRNEYEDYKKEGKGFYLVDFSGNDLDISDIEKIDIECREFVEVNIKDKKSFNEAVNKIERCKNKPVVFGKIKREFKPWFDTLKDKILINKAIIVDDEFIDMPDNVDIESLNIKELLVDYANRQGIDGDLVLSLYKALLNNENWKELLDEYYNTKFRG  366
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357         


Chain B from PDB  Type:PROTEIN  Length:365
 aligned with RAD50_METJA | Q58718 from UniProtKB/Swiss-Prot  Length:1005

    Alignment length:1005
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000     
         RAD50_METJA      1 MSMILKEIRMNNFKSHVNSRIKFEKGIVAIIGENGSGKSSIFEAVFFALFGAGSNFNYDTIITKGKKSVYVELDFEVNGNNYKIIREYDSGRGGAKLYKNGKPYATTISAVNKAVNEILGVDRNMFLNSIYIKQGEIAKFLSLKPSEKLETVAKLLGIDEFEKCYQKMGEIVKEYEKRLERIEGELNYKENYEKELKNKMSQLEEKNKKLMEINDKLNKIKKEFEDIEKLFNEWENKKLLYEKFINKLEERKRALELKNQELKILEYDLNTVVEARETLNRHKDEYEKYKSLVDEIRKIESRLRELKSHYEDYLKLTKQLEIIKGDIEKLKEFINKSKYRDDIDNLDTLLNKIKDEIERVETIKDLLEELKNLNEEIEKIEKYKRICEECKEYYEKYLELEEKAVEYNKLTLEYITLLQEKKSIEKNINDLETRINKLLEETKNIDIESIENSLKEIEEKKKVLENLQKEKIELNKKLGEINSEIKRLKKILDELKEVEGKCPLCKTPIDENKKMELINQHKTQLNNKYTELEEINKKIREIEKDIEKLKKEIDKEENLKTLKTLYLEKQSQIEELELKLKNYKEQLDEINKKISNYVINGKPVDEILEDIKSQLNKFKNFYNQYLSAVSYLNSVDEEGIRNRIKEIENIVSGWNKEKCREELNKLREDEREINRLKDKLNELKNKEKELIEIENRRSLKFDKYKEYLGLTEKLEELKNIKDGLEEIYNICNSKILAIDNIKRKYNKEDIEIYLNNKILEVNKEINDIEERISYINQKLDEINYNEEEHKKIKELYENKRQELDNVREQKTEIETGIEYLKKDVESLKARLKEMSNLEKEKEKLTKFVEYLDKVRRIFGRNGFQAYLREKYVPLIQKYLNEAFSEFDLPYSFVELTKDFEVRVHAPNGVLTIDNLSGGEQIAVALSLRLAIANALIGNRVECIILDEPTVYLDENRRAKLAEIFRKVKSIPQMIIITHHRELEDVADVIINVKKDGNVSKVKING 1005
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee..eeeeeee...eeeee........hhhhhhhhhhhhh..................eeeeeeee....eeeee........eeeee.......hhhhhhhhhh..............ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.....eeeee..eeee....hhhhhhhhhhhhhhhhhhhh.......eeee......hhhhhhhhhhhhhhh....eeeee..hhhhhh.......eeee..eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3av0 B    1 MSMILKEIRMNNFKSHVNSRIKFEKGIVAIIGENGSGKSSIFEAVFFALFGAGSNFNYDTIITKGKKSVYVELDFEVNGNNYKIIREYDSGRGGAKLYKNGKPYATTISAVNKAVNEILGVDRNMFLNSIYIKQGEIAKFLSLKPSEKLETVAKLLGIDEFEKCYQKMGEIVKEYEKRLERIEGELNYK----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RLKEMSNLEKEKEKLTKFVEYLDKVRRIFGRNGFQAYLREKYVPLIQKYLNEAFSEFDLPYSFVELTKDFEVRVHAPNGVLTIDNLSGGEQIAVALSLRLAIANALIGNRVECIILDEPTVYLDENRRAKLAEIFRKVKSIPQMIIITHHRELEDVADVIINVKKDGNVSKVKING 1005
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        |-         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000     
                                                                                                                                                                                                                      189                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              830
   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  (0, 0)

(no "SCOP Domain" information available for 3AV0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AV0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AV0)

(-) Gene Ontology  (15, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MRE11_METJA | Q58719)
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.
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.

Chain B   (RAD50_METJA | Q58718)
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: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: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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  MRE11_METJA | Q58719
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  RAD50_METJA | Q58718
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 Related Entries

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

UniProtKB/Swiss-Prot
        MRE11_METJA | Q58719: 3auz 4tug 4tui 5dny 5f3w
        RAD50_METJA | Q58718: 3aux 3auy 5dny 5f3w

(-) Related Entries Specified in the PDB File

3aux 3auy 3auz