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(-) Description

Title :  CRYSTAL STRUCTURE OF A HAIRPIN EXCHANGE VARIANT (LTX) OF THE TARGETING LINE-1 RETROTRANSPOSON ENDONUCLEASE
 
Authors :  K. Repanas, N. Zingler, L. E. Layer, G. G. Schumann, A. Perrakis, O. Weichenrieder
Date :  17 May 07  (Deposition) - 17 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ape-1 Type, Endonuclease, Retrotransposition, Retrotransposon, Protein Engineering, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Repanas, N. Zingler, L. E. Layer, G. G. Schumann, A. Perrakis, O. Weichenrieder
Determinants For Dna Target Structure Selectivity Of The Human Line-1 Retrotransposon Endonuclease
Nucleic Acids Res. V. 35 4914 2007
PubMed-ID: 17626046  |  Reference-DOI: 10.1093/NAR/GKM516

(-) Compounds

Molecule 1 - LTX
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PET
    Fragment: RESIDUES 1-192,202-238
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:16 , GLY A:17 , LEU A:18 , ASN A:19 , HIS A:45BINDING SITE FOR RESIDUE SO4 A1241
2AC2SOFTWAREHIS A:45 , LYS A:71 , ALA A:72 , TYR A:115 , HOH A:2023BINDING SITE FOR RESIDUE SO4 A1242
3AC3SOFTWAREGLU A:43 , TYR A:115 , ASN A:118 , ASP A:145 , TYR A:193 , HIS A:232 , HOH A:2078BINDING SITE FOR RESIDUE SO4 A1243
4AC4SOFTWAREPRO A:149 , ARG A:155 , HOH A:2045 , HOH A:2079BINDING SITE FOR RESIDUE SO4 A1244
5AC5SOFTWAREHIS B:45 , LYS B:71 , ALA B:72 , TYR B:115BINDING SITE FOR RESIDUE SO4 B1240
6AC6SOFTWAREGLY B:17 , LEU B:18 , ASN B:19 , HIS B:45 , HOH B:2076BINDING SITE FOR RESIDUE SO4 B1241

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V0R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V0R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V0R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V0R)

(-) Exons   (0, 0)

(no "Exon" information available for 2V0R)

(-) 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:235
 aligned with LORF2_HUMAN | O00370 from UniProtKB/Swiss-Prot  Length:1275

    Alignment length:235
                                                                                                                                                                                                                            198                                        
                                                                                                                                                                                                                         197  |                                        
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 |  |  203       213       223       233     
          LORF2_HUMAN     6 SHITILTLNVNGLNSPIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSILDRSTRQKVNKDTQELNSALHQTDLIDIYRTLHPKSTEYTFFSAP--HHTYSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLELR 238
               SCOP domains d2v0ra_ A: automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains 2v0rA00 A:6-240  [code=3.60.10.10, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhh..eeeee......hhhhhh......eeeee........eeeee.....eeeeeeee.....eeeeeeee..eeeeeeeee....hhhhhhhhhhhhhhhhh...eeeeee.....hhhhh......hhhhhhhhhhhhhh.eeehhhhhh.......eeeee..eeeee..eeeeee.hhhh.eeeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v0r A   6 SHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTYVRVRDGHVSQSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLELR 240
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235     


Chain A from PDB  Type:PROTEIN  Length:235
 aligned with Q8TE30_HUMAN | Q8TE30 from UniProtKB/TrEMBL  Length:1275

    Alignment length:235
                                                                                                                                                                                                                            198                                        
                                                                                                                                                                                                                         197  |                                        
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 |  |  203       213       223       233     
         Q8TE30_HUMAN     6 SHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTFFSAP--HHTYSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLELR 238
               SCOP domains d2v0ra_ A: automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains 2v0rA00 A:6-240  [code=3.60.10.10, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhh..eeeee......hhhhhh......eeeee........eeeee.....eeeeeeee.....eeeeeeee..eeeeeeeee....hhhhhhhhhhhhhhhhh...eeeeee.....hhhhh......hhhhhhhhhhhhhh.eeehhhhhh.......eeeee..eeeee..eeeeee.hhhh.eeeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v0r A   6 SHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTYVRVRDGHVSQSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLELR 240
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235     


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with LORF2_HUMAN | O00370 from UniProtKB/Swiss-Prot  Length:1275

    Alignment length:234
                                                                                                                                                                                                                            198                                       
                                                                                                                                                                                                                         197  |                                       
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 |  |  203       213       223       233    
          LORF2_HUMAN     6 SHITILTLNVNGLNSPIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSILDRSTRQKVNKDTQELNSALHQTDLIDIYRTLHPKSTEYTFFSAP--HHTYSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLEL 237
               SCOP domains d2v0rb_ B: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 2v0rB00 B:6-239  [code=3.60.10.10, no name defined]                                                                                                                                                                                        CATH domains
           Pfam domains (1) -----Exo_endo_phos-2v0rB01 B:11-232                                                                                                                                                                                                ------- Pfam domains (1)
           Pfam domains (2) -----Exo_endo_phos-2v0rB02 B:11-232                                                                                                                                                                                                ------- Pfam domains (2)
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhh..eeeee......hhhhhh......eeeee........eeeee.....eeeeeeee.....eeeeeeee..eeeeeeeee....hhhhhhhhhhhhhhhhh...eeeeee.....hhhhh......hhhhhhhhhhhhhh.eeehhhhhh.......eeeee..eeeee..eeeeee.hhhhhh..eeee........eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2v0r B   6 SHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTYVRVRDGHVSQSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLEL 239
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235    


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with Q8TE30_HUMAN | Q8TE30 from UniProtKB/TrEMBL  Length:1275

    Alignment length:234
                                                                                                                                                                                                                            198                                       
                                                                                                                                                                                                                         197  |                                       
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 |  |  203       213       223       233    
         Q8TE30_HUMAN     6 SHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTFFSAP--HHTYSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLEL 237
               SCOP domains d2v0rb_ B: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 2v0rB00 B:6-239  [code=3.60.10.10, no name defined]                                                                                                                                                                                        CATH domains
           Pfam domains (1) -----Exo_endo_phos-2v0rB01 B:11-232                                                                                                                                                                                                ------- Pfam domains (1)
           Pfam domains (2) -----Exo_endo_phos-2v0rB02 B:11-232                                                                                                                                                                                                ------- Pfam domains (2)
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhh..eeeee......hhhhhh......eeeee........eeeee.....eeeeeeee.....eeeeeeee..eeeeeeeee....hhhhhhhhhhhhhhhhh...eeeeee.....hhhhh......hhhhhhhhhhhhhh.eeehhhhhh.......eeeee..eeeee..eeeeee.hhhhhh..eeee........eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2v0r B   6 SHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTYVRVRDGHVSQSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLEL 239
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Exo_endo_phos] (21)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LORF2_HUMAN | O00370)
molecular function
    GO:0003964    RNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
    GO:0009036    Type II site-specific deoxyribonuclease activity    Catalysis of the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates and 3' hydroxyls. Cleavage is dependent on the presence in the DNA of a specific recognition site; cleavage occurs at or very near this recognition site.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0032199    reverse transcription involved in RNA-mediated transposition    The synthesis of DNA from an RNA transposon intermediate.
    GO:0032197    transposition, RNA-mediated    Any process involved in a type of transpositional recombination which occurs via an RNA intermediate.

Chain A,B   (Q8TE30_HUMAN | Q8TE30)
molecular function
    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).

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 Related Entries

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

UniProtKB/Swiss-Prot
        LORF2_HUMAN | O00370: 1vyb 2v0s
        Q8TE30_HUMAN | Q8TE30: 2v0s

(-) Related Entries Specified in the PDB File

1vyb ENDONUCLEASE DOMAIN OF HUMAN LINE1 ORF2P
2v0s CRYSTAL STRUCTURE OF A HAIRPIN EXCHANGE VARIANT (LR1) OF THE TARGETING LINE-1 RETROTRANSPOSON ENDONUCLEASE