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(-) Description

Title :  MOUSE TREX1 D200N MUTANT
 
Authors :  S. L. Bailey, S. Harvey, F. W. Perrino, T. Hollis
Date :  12 Oct 11  (Deposition) - 28 Dec 11  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rnase H Fold, 3' Exonuclease, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. L. Bailey, S. Harvey, F. W. Perrino, T. Hollis
Defects In Dna Degradation Revealed In Crystal Structures O Trex1 Exonuclease Mutations Linked To Autoimmune Disease.
Dna Repair V. 11 65 2012
PubMed-ID: 22071149  |  Reference-DOI: 10.1016/J.DNAREP.2011.10.007

(-) Compounds

Molecule 1 - THREE PRIME REPAIR EXONUCLEASE 1
    ChainsB, A
    EC Number3.1.11.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneTREX1
    MutationYES
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Synonym3'-5' EXONUCLEASE TREX1
 
Molecule 2 - 5'-D(*GP*AP*CP*G)-3'
    ChainsC, D
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1BU12Ligand/Ion1,4-BUTANEDIOL
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:192 , ASP B:193 , GLU B:198 , GLY B:199 , LEU B:202BINDING SITE FOR RESIDUE BU1 B 315
2AC2SOFTWAREASP A:193 , THR A:196 , GLU A:198 , HOH A:360BINDING SITE FOR RESIDUE BU1 A 315
3AC3SOFTWAREASP B:18 , HOH B:332 , HOH B:363 , HOH B:370 , DC C:3 , DG C:4BINDING SITE FOR RESIDUE MG C 5
4AC4SOFTWAREASP A:18 , HOH A:331 , HOH A:359 , HOH A:381 , DC D:3 , DG D:4BINDING SITE FOR RESIDUE MG D 5

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U6F)

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U6F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U6F)

(-) Exons   (0, 0)

(no "Exon" information available for 3U6F)

(-) 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:217
 aligned with TREX1_MOUSE | Q91XB0 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:228
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226        
          TREX1_MOUSE     7 PHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
               SCOP domains d3u6fa_ A: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeee..hhhhh..eeeeeeeeeehhhhh.---..............eeeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhhh.--------....hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3u6f A   7 PHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALEN---SQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQA--------RKSYSLGSIYTRLYWQAPTDSHTAEGNVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
                                    16        26        36        46   |    56        66        76        86        96       106       116       126       136       146       156        |-       176       186       196       206       216       226        
                                                                  46  50                                                                                                                165      174                                                            

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

    Alignment length:230
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236
          TREX1_MOUSE     7 PHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYGTP 236
               SCOP domains d3u6fb_ B: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee..hhhhh..eeeeeeeeee.hhh----................eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhhh..--------...hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhh..ee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u6f B   7 PHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRAL----ISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQAS--------KSYSLGSIYTRLYWQAPTDSHTAEGNVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYGTP 236
                                    16        26        36       | -  |     56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236
                                                                44   49                                                                                                                  166      175                                                             

Chain C from PDB  Type:DNA  Length:4
                                    
                 3u6f C   1 GACG   4

Chain D from PDB  Type:DNA  Length:4
                                    
                 3u6f D   1 GACG   4

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U6F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U6F)

(-) 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 | Q91XB02ioc 2o4g 2o4i 2oa8 3b6o 3b6p 3mxi 3mxj 3mxm 3u3y 4ynq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3U6F)