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(-) Description

Title :  CRYSTAL STRUCTURE OF MRE11 FROM THERMOTOGA MARITIMA MSB8 (TM1635) AT 2.20 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  11 Jun 07  (Deposition) - 26 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Das, D. Moiani, H. L. Axelrod, M. D. Miller, D. Mcmullan, K. K. Jin, P. Abdubek, T. Astakhova, P. Burra, D. Carlton, H. J. Chiu, T. Clayton, M. C. Deller, L. Duan, D. Ernst, J. Feuerhelm, J. C. Grant, A. Grzechnik S. K. Grzechnik, G. W. Han, L. Jaroszewski, H. E. Klock, M. W. Knuth, P. Kozbial, S. S. Krishna, A. Kumar, D. Marciano, A. T. Morse, E. Nigoghossian, L. Okach, J. Paulsen, R. Reyes, C. L. Rife, N. Sefcovic, H. J. Tien, C. B. Trame, H. Van Den Bedem, D. Weekes, Q. Xu K. O. Hodgson, J. Wooley, M. A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley, J. A. Tainer, I. A. Wilson
Crystal Structure Of The First Eubacterial Mre11 Nuclease Reveals Novel Features That May Discriminate Substrates During Dna Repair.
J. Mol. Biol. V. 397 647 2010
PubMed-ID: 20122942  |  Reference-DOI: 10.1016/J.JMB.2010.01.049

(-) Compounds

Molecule 1 - EXONUCLEASE, PUTATIVE
    Atcc43589
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidSPEEDET
    Expression System StrainHK100
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-324
    GeneTM_1635
    Organism ScientificTHERMOTOGA MARITIMA MSB8
    Organism Taxid243274
    StrainMSB8, DSM 3109, JCM 10099

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2Q8U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q8U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:226 -Pro A:227
2Gln B:226 -Pro B:227

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q8U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q8U)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q8U)

(-) Sequences/Alignments

Asymmetric 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:308
 aligned with Q9X1X0_THEMA | Q9X1X0 from UniProtKB/TrEMBL  Length:385

    Alignment length:329
                                 1                                                                                                                                                                                                                                                                                                                                   
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315         
         Q9X1X0_THEMA     - -----MINLKELKILHTSDWHLGVTSWTSSRPVDRREELKKALDKVVEEAEKREVDLILLTGDLLHSRNNPSVVALHDLLDYLKRMMRTAPVVVLPGNHDWKGLKLFGNFVTSISSDITFVMSFEPVDVEAKRGQKVRILPFPYPDESEALRKNEGDFRFFLESRLNKLYEEALKKEDFAIFMGHFTVEGLAGYAGIEQGREIIINRALIPSVVDYAALGHIHSFREIQKQPLTIYPGSLIRIDFGEEADEKGAVFVELKRGEPPRYERIDASPLPLKTLYYKKIDTSALKSIRDFCRNFPGYVRVVYEEDSGILPDLMGEIDNLVKIE 324
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------2q8uA01 A:5-270  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                       2q8uA02 A:271-324                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee......ee......eehhhhhhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhhhh.eee...------hhhhhhhhhhhh..eee......eeee.....eeeeeee...-------...hhhhhhhhhhhhhhhhhhhh...eeeeeee.ee....--------...eehhhhh.....eeeee.....eeee....eee.......hhhhh....eeeeeeee.....eeeeee.....eeeeeeee.hhhhhhhhhhhhhh...eeeeeeee......hhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q8u A  -4 HHHHHVINLKELKILHTSDWHLGVTSWTSSRPVDRREELKKALDKVVEEAEKREVDLILLTGDLLHSRNNPSVVALHDLLDYLKRmmRTAPVVVLPG------LKLFGNFVTSISSDITFVmSFEPVDVEAKRGQKVRILPFPYP-------KNEGDFRFFLESRLNKLYEEALKKEDFAIFmGHFTVEGLA--------REIIINRALIPSVVDYAALGHIHSFREIQKQPLTIYPGSLIRIDFGEEADEKGAVFVELKRGEPPRYERIDASPLPLKTLYYKKIDTSALKSIRDFCRNFPGYVRVVYEEDSGILPDLmGEIDNLVKIE 324
                                     5        15        25        35        45        55        65        75     || 85      |  -   |   105       115 |     125       135    |    -  |    155       165       175  |    185 |       -|      205       215       225       235       245       255       265       275       285       295       305       315         
                                                                                                                81-MSE     92     99               117-MSE                140     148                           178-MSE  187      196                                                                                                                   314-MSE      
                                                                                                                 82-MSE                                                                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:294
 aligned with Q9X1X0_THEMA | Q9X1X0 from UniProtKB/TrEMBL  Length:385

    Alignment length:318
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316        
         Q9X1X0_THEMA     7 LKILHTSDWHLGVTSWTSSRPVDRREELKKALDKVVEEAEKREVDLILLTGDLLHSRNNPSVVALHDLLDYLKRMMRTAPVVVLPGNHDWKGLKLFGNFVTSISSDITFVMSFEPVDVEAKRGQKVRILPFPYPDESEALRKNEGDFRFFLESRLNKLYEEALKKEDFAIFMGHFTVEGLAGYAGIEQGREIIINRALIPSVVDYAALGHIHSFREIQKQPLTIYPGSLIRIDFGEEADEKGAVFVELKRGEPPRYERIDASPLPLKTLYYKKIDTSALKSIRDFCRNFPGYVRVVYEEDSGILPDLMGEIDNLVKIE 324
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2q8uB01 B:7-270  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                     2q8uB02 B:271-324                                      CATH domains
           Pfam domains (1) Metallophos-2q8uB01 B:7-220                                                                                                                                                                                           -------------------------------------------------SbcD_C-2q8uB03 B:270-324                                Pfam domains (1)
           Pfam domains (2) Metallophos-2q8uB02 B:7-220                                                                                                                                                                                           -------------------------------------------------SbcD_C-2q8uB04 B:270-324                                Pfam domains (2)
         Sec.struct. author .eeeeee......ee......eehhhhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhhh.eee.....----hhhhhhhhhhhh..eee......eeee.....eeeeeee...---------.hhhhhhhhhhhhhhhhhhhh...eeeeeee.ee...---------...eehhhhh.....eeeee.....eeee...eeee.......hhhhh....eeeeee.......eeeeee.....eeeeee...hhhhhhhhhhhhhhh..eeeeee.......--.......eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q8u B   7 LKILHTSDWHLGVTSWTSSRPVDRREELKKALDKVVEEAEKREVDLILLTGDLLHSRNNPSVVALHDLLDYLKRmmRTAPVVVLPGNH----LKLFGNFVTSISSDITFVmSFEPVDVEAKRGQKVRILPFPYP---------EGDFRFFLESRLNKLYEEALKKEDFAIFmGHFTVEGL---------REIIINRALIPSVVDYAALGHIHSFREIQKQPLTIYPGSLIRIDFGEEADEKGAVFVELKRGEPPRYERIDASPLPLKTLYYKKIDTSALKSIRDFCRNFPGYVRVVYEEDSGIL--LmGEIDNLVKIE 324
                                    16        26        36        46        56        66        76    ||  86       | -  |    106       116|      126       136   |     -   |   156       166       176 |     186       196       206       216       226       236       246       256       266       276       286       296       306   |  |316        
                                                                                                     81-MSE       94   99               117-MSE                140       150                         178-MSE 186       196                                                                                                               310  ||          
                                                                                                      82-MSE                                                                                                                                                                                                                                313|          
                                                                                                                                                                                                                                                                                                                                             314-MSE      

   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 2Q8U)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9X1X0_THEMA | Q9X1X0)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    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/TrEMBL
        Q9X1X0_THEMA | Q9X1X03qf7 3qg5 3thn 3tho 4nzv 4o24 4o43 4o4k 4o5g 4w9m

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