Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  THE HUMAN TREX2 3' EXONUCLEASE STRUCTURE SUGGESTS A MECHANISM FOR EFFICIENT NON-PROCESSIVE DNA CATALYSIS
 
Authors :  F. W. Perrino, S. Harvey, S. Mcmillin, T. Hollis
Date :  14 Dec 04  (Deposition) - 25 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trex2, Exonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. W. Perrino, S. Harvey, S. Mcmillin, T. Hollis
The Human Trex2 3' -> 5'-Exonuclease Structure Suggests A Mechanism For Efficient Nonprocessive Dna Catalysis.
J. Biol. Chem. V. 280 15212 2005
PubMed-ID: 15661738  |  Reference-DOI: 10.1074/JBC.M500108200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THREE PRIME REPAIR EXONUCLEASE 2
    Chains: A, B
    EC Number: 3.1.11.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: TREX2 EXONUCLEASE
    Gene: TREX2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 3'-5' EXONUCLEASE TREX2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1Y97)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y97)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:110 -Pro A:111
2Gly B:110 -Pro B:111

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_025211R180CTREX2_HUMANPolymorphism35132777A/BR137C
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y97)

(-) Exons   (2, 3)

Asymmetric/Biological Unit (2, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003702321ENSE00001452132X:152736045-152735908138TREX2_HUMAN-00--
1.2ENST000003702322ENSE00002146988X:152734719-152734604116TREX2_HUMAN-00--
1.3ENST000003702323ENSE00002192240X:152730513-15273044668TREX2_HUMAN-00--
1.4ENST000003702324ENSE00002160169X:152728129-15272806862TREX2_HUMAN-00--
1.5ENST000003702325ENSE00002164724X:152722686-15272259592TREX2_HUMAN-00--
1.6ENST000003702326ENSE00002149004X:152722109-152721951159TREX2_HUMAN-00--
1.7ENST000003702327ENSE00002194113X:152721822-152721723100TREX2_HUMAN-00--
1.8bENST000003702328bENSE00002201070X:152721106-152721000107TREX2_HUMAN-00--
1.10ENST0000037023210ENSE00002188618X:152719966-152719852115TREX2_HUMAN-00--
1.11aENST0000037023211aENSE00002141124X:152713367-152713206162TREX2_HUMAN1-32321A:-1-0
-		2
-
1.14bENST0000037023214bENSE00002147397X:152710922-152710178745TREX2_HUMAN32-2792482A:1-228 (gaps)
B:3-228 (gaps)		228
226

(-) 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:214
 aligned with TREX2_HUMAN | Q9BQ50 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:268
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263        
          TREX2_HUMAN     4 AGSPLPRSSWPRMDDCGSRSRCSPTLCSSLRTCYPRGNITMSEAPRAETFVFLDLEATGLPSVEPEIAELSLFAVHRSSLENPEHDESGALVLPRVLDKLTLCMCPERPFTAKASEITGLSSEGLARCRKAGFDGAVVRTLQAFLSRQAGPICLVAHNGFDYDFPLLCAELRRLGARLPRDTVCLDTLPALRGLDRAHSHGTRARGRQGYSLGSLFHRYFRAEPSAAHSAEGDVHTLLLIFLHRAAELLAWADEQARGWAHIEPMYLP 271
               SCOP domains --                                      d1y97a1 A:1-228 Three prime repair exonucleas   e 2, TREX2                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..--------------------------------------........eeeeeeeee..hhhhh..eeeeeeeeeehhhhh....---.........eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhh........eeeehhhhhhhhhhhh----------..hhhhhhhhhhh....---hhhhhhhhhhhhhhhhhhhhhhhhhhhhee.hhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11a  PDB: A:-1-0      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.14b  PDB: A:1-228 (gaps) UniProt: 32-279 [INCOMPLETE]                                                                                                                                                                                     Transcript 1 (2)
                 1y97 A  -1 AG--------------------------------------mSEAPRAETFVFLDLEATGLPSVEPEIAELSLFAVHRSSLENPEH---GALVLPRVLDKLTLCmCPERPFTAKASEITGLSSEGLARCRKAGFDGAVVRTLQAFLSRQAGPICLVAHNGFDYDFPLLCAELRRLGARLPRDTVCLDTLPALRGLDRAH----------GYSLGSLFHRYFRAEPS---SAEGDVHTLLLIFLHRAAELLAWADEQARGWAHIEPmYLP 228
                             |       -         -         -         -|       10        20        30        40    |   50        60   |    70        80        90       100       110       120       130       140       150       | -       170       180    |  190       200       210       220    |   
                             0                                      1-MSE                                      45  49             64-MSE                                                                                       158        169             185 189                                 225-MSE


Chain B from PDB  Type:PROTEIN  Length:211
 aligned with TREX2_HUMAN | Q9BQ50 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:226
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265      
          TREX2_HUMAN    46 EAPRAETFVFLDLEATGLPSVEPEIAELSLFAVHRSSLENPEHDESGALVLPRVLDKLTLCMCPERPFTAKASEITGLSSEGLARCRKAGFDGAVVRTLQAFLSRQAGPICLVAHNGFDYDFPLLCAELRRLGARLPRDTVCLDTLPALRGLDRAHSHGTRARGRQGYSLGSLFHRYFRAEPSAAHSAEGDVHTLLLIFLHRAAELLAWADEQARGWAHIEPMYLP 271
               SCOP domains d1y97b_ B: Three prime repair exonuclease 2, TREX2                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------RNase_T-1y97B01 B:11-201                                                                                                                                                                       --------------------------- Pfam domains (1)
           Pfam domains (2) --------RNase_T-1y97B02 B:11-201                                                                                                                                                                       --------------------------- Pfam domains (2)
         Sec.struct. author ......eeeeeeeee..hhhhh..eeeeeeeeeehhhhhh.ee.....ee.....eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh.........eeeehhhhhhhhhh------------..hhhhhhhhhh....---.hhhhhhhhhhhhhhhhhhhhhhhhhhhhee.hhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.14b  PDB: B:3-228 (gaps) UniProt: 32-279 [INCOMPLETE]                                                                                                                                                                       Transcript 1 (2)
                 1y97 B   3 EAPRAETFVFLDLEATGLPSVEPEIAELSLFAVHRSSLENPEHDESGALVLPRVLDKLTLCmCPERPFTAKASEITGLSSEGLARCRKAGFDGAVVRTLQAFLSRQAGPICLVAHNGFDYDFPLLCAELRRLGARLPRDTVCLDTLPALRGLDR------------GYSLGSLFHRYFRAEP---HSAEGDVHTLLLIFLHRAAELLAWADEQARGWAHIEPmYLP 228
                                    12        22        32        42        52        62 |      72        82        92       102       112       122       132       142       152   |     -      |172       182 |   | 192       202       212       222  |   
                                                                                        64-MSE                                                                                     156          169            184 188                                  225-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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Y97)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: RNase_H (288)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TREX2_HUMAN | Q9BQ50)
molecular function
    GO:0008296    3'-5'-exodeoxyribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a DNA molecule.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) 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.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
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: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: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: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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1y97)
 
  Cis Peptide Bonds
    Gly A:110 - Pro A:111   [ RasMol ]  
    Gly B:110 - Pro B:111   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1y97
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TREX2_HUMAN | Q9BQ50
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.11.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TREX2_HUMAN | Q9BQ50
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1Y97)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1Y97)