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(-) Description

Title :  THE CRYSTAL STRUCTURE OF I-LTRI
 
Authors :  A. N. S. Mak, R. Takeuchi, D. R. Edgell, B. L. Stoddard
Date :  22 Mar 11  (Deposition) - 20 Jul 11  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Homing Endonuclease, Gene Therapy, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Takeuchi, A. R. Lambert, A. N. Mak, K. Jacoby, R. J. Dickson, G. B. Gloor, A. M. Scharenberg, D. R. Edgell, B. L. Stoddard
Tapping Natural Reservoirs Of Homing Endonucleases For Targeted Gene Modification.
Proc. Natl. Acad. Sci. Usa V. 108 13077 2011
PubMed-ID: 21784983  |  Reference-DOI: 10.1073/PNAS.1107719108

(-) Compounds

Molecule 1 - RIBOSOMAL PROTEIN 3/HOMING ENDONUCLEASE-LIKE FUSION PROTEIN
    Chains: A
    EC Number: 3.1.21.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-200-D-TOPO
    Expression System Strain: RIL (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: I-LTRI (UNP RESIDUES 398-712)
    Gene: RPS3/HEG FUSION
    Organism Scientific: LEPTOGRAPHIUM TRUNCATUM
    Organism Taxid: 330483
 
Molecule 2 - DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)- 3')
    Chains: B
    Engineered: YES
    Other Details: SYNTHETIC
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*AP*GP*GP*AP*GP*CP*AP*TP*TP*TP*G)-3')
    Chains: C
    Engineered: YES
    Other Details: SYNTHETIC
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(*CP*AP*AP*AP*TP*GP*CP*TP*CP*CP*TP*AP*TP*AP*C)- 3')
    Chains: D
    Engineered: YES
    Other Details: SYNTHETIC
    Synthetic: YES
 
Molecule 5 - DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*AP*GP*AP*CP*C)-3')
    Chains: E
    Engineered: YES
    Other Details: SYNTHETIC
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
2MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:29 , GLU A:184 , MG A:317 , DA C:17 , DC D:15 , DG E:16BINDING SITE FOR RESIDUE MN A 316
2AC2SOFTWARELYS A:274 , HOH A:320 , HOH A:336 , DT B:16 , DG E:16 , HOH E:28BINDING SITE FOR RESIDUE MG B 17
3AC3SOFTWAREHOH B:21 , DA C:17 , DC D:15 , HOH D:22 , DG E:16BINDING SITE FOR RESIDUE MG E 2
4AC4SOFTWAREALA A:28 , GLU A:184 , MN A:316 , HOH A:322 , HOH A:323 , DA C:17 , DC D:15BINDING SITE FOR RESIDUE MG A 317

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R7P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3R7P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R7P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R7P)

(-) Exons   (0, 0)

(no "Exon" information available for 3R7P)

(-) 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:292
 aligned with C7SWF3_9PEZI | C7SWF3 from UniProtKB/TrEMBL  Length:712

    Alignment length:301
                                   421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711 
         C7SWF3_9PEZI   412 DNISPWTITGFADAESSFMLTVSKDSKRNTGWSVRPRFRIGLHNKDVTILKSIREYLGAGIITSDIDARIRFESLKELEVVINHFDKYPLITQKRADYLLFKKAFYLIKNKEHLTEEGLNQILTLKASLNLGLSEELKEAFPNTIPAERLLVTGQEIPDSNWVAGFTAGEGSFYIRIAKNSTLKTGYQVQSVFQITQDTRDIELMKNLISYLNCGNIRIRKYKGSEGIHDTCVDLVVTNLNDIKEKIIPFFNKNHIIGVKLQDYRDWCKVVTLIDNKEHLTSEGLEKIQKIKEGMNRGRSL 712
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhheeeeeeee.......eeeeeeeeeeehhhhhhhhhhhhhhhh..eeee...eeeee.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhh.................hhhhhhhhhhhheeeeeeeee.......eeeeeeeeeeee..hhhhhhhhhhhhh..eeeee.---------.eeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r7p A  15 DNISPWTITGFADAESSFMLTVSKDSKRNTGWSVRPRFRIGLHNKDVTILKSIREYLGAGIITSDIDARIRFESLKELEVVINHFDKYPLITQKRADYLLFKKAFYLIKNKEHLTEEGLNQILTLKASLNLGLSEELKEAFPNTIPAERLLVTGQEIPDSNWVAGFTAGEGSFYIRIAKNSTLKTGYQVQSVFQITQDTRDIELMKNLISYLNCGNIRIRK---------TCVDLVVTNLNDIKEKIIPFFNKNHIIGVKLQDYRDWCKVVTLIDNKEHLTSEGLEKIQKIKEGMNRGRSL 315
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234|        -|      254       264       274       284       294       304       314 
                                                                                                                                                                                                                                                      235       245                                                                      


Chain B from PDB  Type:DNA  Length:16
                                                
                 3r7p B   1 GGTCTAAACGTCGTAT  16
                                    10      


Chain C from PDB  Type:DNA  Length:11
                                           
                 3r7p C  17 AGGAGCATTTG  27
                                    26 


Chain D from PDB  Type:DNA  Length:15
                                               
                 3r7p D   1 CAAATGCTCCTATAC  15
                                    10     


Chain E from PDB  Type:DNA  Length:12
                                            
                 3r7p E  16 GACGTTTAGACC  27
                                    25
   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  (0, 0)

(no "SCOP Domain" information available for 3R7P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R7P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R7P)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (C7SWF3_9PEZI | C7SWF3)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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  3r7p
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