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(-) Description

Title :  STRUCTURE OF TREX1 IN COMPLEX WITH DNA
 
Authors :  M. Brucet, M. J. Macias, I. Fita, A. Celada
Date :  04 Dec 06  (Deposition) - 13 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Trex1, Exonuclease, Dnaq, Dna Complex, Ww Motif, Protein-Protein Interaction, Polyproline Binding Motif, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Brucet, J. Querol-Audi, M. Serra, X. Ramirez-Espain, K. Bertlik, L. Ruiz, J. Lloberas, M. J. Macias, I. Fita, A. Celada
Structure Of The Dimeric Exonuclease Trex1 In Complex With Dna Displays A Proline-Rich Binding Site For Ww Domains.
J. Biol. Chem. V. 282 14547 2007
PubMed-ID: 17355961  |  Reference-DOI: 10.1074/JBC.M700236200

(-) Compounds

Molecule 1 - 5'-D(*GP*CP*TP*AP*GP*GP*CP*AP*GP*GP*AP*AP*CP*CP*CP*CP*TP*CP *CP*TP*CP*CP*CP*CP*T)-3'
    Chains: C, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - THREE PRIME REPAIR EXONUCLEASE 1
    Chains: A, B
    EC Number: 3.1.11.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PETM-10
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: TREX1 EXONUCLEASE
    Gene: TREX1
    Mutation: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: 3'-5' EXONUCLEASE TREX1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2O4I)

(-) Sites  (0, 0)

(no "Site" information available for 2O4I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O4I)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1His A:53 -Pro A:54
2Gln A:117 -Pro A:118
3His B:53 -Pro B:54
4Gln B:117 -Pro B:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O4I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O4I)

(-) Exons   (0, 0)

(no "Exon" information available for 2O4I)

(-) 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:218
 aligned with TREX1_MOUSE | Q91XB0 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:226
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228      
         TREX1_MOUSE      9 GHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG  234
               SCOP domains d2o4ia1 A:9-234 Three prime repair exonuclease 1, TREX1                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..hhhhh..eeeeeeeeeehhhhhh..................eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh.........eeeehhhhhhhhhhh.--------...hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.hhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2o4i A    9 GHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQAS--------KSYSLGSIYTRLYWQAPTDSATAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG  234
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       | -      |178       188       198       208       218       228      
                                                                                                                                                                                       166      175                                                           


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with TREX1_MOUSE | Q91XB0 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:226
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228      
         TREX1_MOUSE      9 GHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG  234
               SCOP domains d2o4ib1 B:9-234 Three prime repair exonuclease 1, TREX1                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..hhhhh..eeeeeeeeeehhhhhh..................eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh.........eeeehhhhhhhhhhh--------....hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.hhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2o4i B    9 GHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQA--------RKSYSLGSIYTRLYWQAPTDSATAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG  234
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158      |  -     | 178       188       198       208       218       228      
                                                                                                                                                                                      165      174                                                            


Chain C from PDB  Type:DNA  Length:4
                                     
                2o4i C 1001 CCCT 1004


Chain D from PDB  Type:DNA  Length:4
                                     
                2o4i D 1001 CCCT 1004
   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) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O4I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2O4I)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TREX1_MOUSE | Q91XB0)
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:0008296    3'-5'-exodeoxyribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a DNA molecule.
    GO:0032405    MutLalpha complex binding    Interacting selectively and non-covalently with the mismatch repair complex MutLalpha.
    GO:0032407    MutSalpha complex binding    Interacting selectively and non-covalently with the mismatch repair complex MutSalpha.
    GO:0032558    adenyl deoxyribonucleotide binding    Interacting selectively and non-covalently with an adenyl deoxyribonucleotide, any compound consisting of adenosine esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0008853    exodeoxyribonuclease III activity    Catalysis of the degradation of double-stranded DNA. It acts progressively in a 3' to 5' direction, releasing 5'-phosphomononucleotides.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
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:0035458    cellular response to interferon-beta    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 an interferon-beta stimulus. Interferon-beta is a type I interferon.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TREX1_MOUSE | Q91XB0: 2ioc 2o4g 2oa8 3b6o 3b6p 3mxi 3mxj 3mxm 3u3y 3u6f 4ynq

(-) Related Entries Specified in the PDB File

1y97 HOMOLOGUE PROTEIN
2o4g THE SAME PROTEIN COMPLEXED WITH A NUCLEOTIDE