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(-) Description

Title :  CRYSTAL STRUCTURE OF MTREX1 WITH SSDNA
 
Authors :  U. De Silva, T. Hollis
Date :  15 Dec 06  (Deposition) - 20 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Poly-Proline Helix, Ssdna Complex, Dnaq Family, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. De Silva, S. Choudhury, S. L. Bailey, S. Harvey, F. W. Perrino, T. Hollis
The Crystal Structure Of Trex1 Explains The 3' Nucleotide Specificity And Reveals A Polyproline Ii Helix For Protein Partnering.
J. Biol. Chem. V. 282 10537 2007
PubMed-ID: 17293595  |  Reference-DOI: 10.1074/JBC.M700039200

(-) Compounds

Molecule 1 - 5'-D(*GP*AP*CP*G)-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 Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET-28
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL FRAGMENT, RESIDUES 5-234
    Gene: TREX1
    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  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:18 , GLU B:20 , ASP B:200 , DG C:4 , HOH C:97 , CA C:302BINDING SITE FOR RESIDUE CA B 301
2AC2SOFTWAREASP B:18 , CA B:301 , HOH B:329 , HOH B:330 , HOH B:418 , DC C:3 , DG C:4BINDING SITE FOR RESIDUE CA C 302
3AC3SOFTWAREASP A:18 , CA A:402 , HOH A:406 , HOH A:430 , HOH A:471 , DC D:3 , DG D:4BINDING SITE FOR RESIDUE CA D 401
4AC4SOFTWAREASP A:18 , GLU A:20 , HIS A:195 , ASP A:200 , DG D:4 , CA D:401BINDING SITE FOR RESIDUE CA A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OA8)

(-) 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 2OA8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OA8)

(-) Exons   (0, 0)

(no "Exon" information available for 2OA8)

(-) 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:220
 aligned with TREX1_MOUSE | Q91XB0 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:231
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234 
          TREX1_MOUSE     5 TLPHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYGT 235
               SCOP domains d2oa8a_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee..hhhhh..eeeeeeeeeehhhhh..---..............eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhhhhh--------...hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oa8 A   5 TLPHGHmQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENT---QGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQAS--------KSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPmYGT 235
                                  | 14        24        34        44  |   | 54        64        74        84        94       104       114       124       134       144       154       164 |       -|      184       194       204       214       224       234 
                                 11-MSE                              47  51                                                                                                                166      175                                                      232-MSE


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with TREX1_MOUSE | Q91XB0 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:233
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233   
          TREX1_MOUSE     4 QTLPHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYGTP 236
               SCOP domains d2oa8b_ B: automated matches                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeee..hhhhh..eeeeeeeeee.hhhh...................eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhhhh.-------....hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.hhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oa8 B   4 QTLPHGHmQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQAS-------RKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPmYGTA 236
                                   |13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163  |      -|      183       193       203       213       223       233   
                                  11-MSE                                                                                                                                                    166     174                                                       232-MSE


Chain C from PDB  Type:DNA  Length:4
                                    
                 2oa8 C   1 GACG   4


Chain D from PDB  Type:DNA  Length:4
                                    
                 2oa8 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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OA8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OA8)

(-) 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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  2oa8
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  3.1.11.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        TREX1_MOUSE | Q91XB0: 2ioc 2o4g 2o4i 3b6o 3b6p 3mxi 3mxj 3mxm 3u3y 3u6f 4ynq

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2OA8)