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(-) Description

Title :  CRYSTAL STRUCTURE OF T7 ENDO I RESOLVASE IN COMPLEX WITH A HOLLIDAY JUNCTION
 
Authors :  J. M. Hadden, A. C. Declais, S. B. Carr, D. M. Lilley, S. E. Phillips
Date :  05 Apr 07  (Deposition) - 30 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,Y,Z
Keywords :  Hydrolase, Holliday Junction Resolvase, Homodimer, Domain Swapped, Composite Active Site, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Hadden, A. C. Declais, S. B. Carr, D. M. Lilley, S. E. Phillips
The Structural Basis Of Holliday Junction Resolution By T7 Endonuclease I.
Nature V. 449 621 2007
PubMed-ID: 17873858  |  Reference-DOI: 10.1038/NATURE06158

(-) Compounds

Molecule 1 - ENDODEOXYRIBONUCLEASE 1
    Chains: A, B
    EC Number: 3.1.21.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 DE3 (PLYSS)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 3
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE T7
    Organism Taxid: 10760
    Synonym: ENDODEOXYRIBONUCLEASE I, ENDONUCLEASE
 
Molecule 2 - 27-MER
    Chains: Z
    Engineered: YES
    Other Details: DNA HOLLIDAY JUNCTION
    Synthetic: YES
 
Molecule 3 - 27-MER
    Chains: Y
    Engineered: YES
    Other Details: DNA HOLLIDAY JUNCTION
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABYZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION

(-) Sites  (0, 0)

(no "Site" information available for 2PFJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PFJ)

(-) 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:129
 aligned with ENDO_BPT7 | P00641 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:129
                                    26        36        46        56        66        76        86        96       106       116       126       136         
            ENDO_BPT7    17 SGLEDKVSKQLESKGIKFEYEEWKVPYVIPASNHTYTPDFLLPNGIFVETKGLWESDDRKKHLLIREQHPELDIRIVFSSSRTKLYKGSPTSYGEFCEKHGIKFADKLIPAEWIKEPKKEVPFDRLKRK 145
               SCOP domains d2pfja_ A: automated matches                                                                                                      SCOP domains
               CATH domains 2pfjA00 A:17-145  [code=3.40.91.30, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.....ee..eeeeeee..eeeee...ee.............hhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhh..eee...hhhhhhh.....hhhhhee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pfj A  17 SGLEDKVSKQLESKGIKFEYEEWKVPYVIPASNHTYTPDFLLPNGIFVETAGLWESDDRKKHLLIREQHPELDIRIVFSSSRTKLYKGSPTSYGEFCEKHGIKFADKLIPAEWIKEPKKEVPFDRLKRK 145
                                    26        36        46        56        66        76        86        96       106       116       126       136         


Chain B from PDB  Type:PROTEIN  Length:130
 aligned with ENDO_BPT7 | P00641 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:130
                                    25        35        45        55        65        75        85        95       105       115       125       135       145
            ENDO_BPT7    16 RSGLEDKVSKQLESKGIKFEYEEWKVPYVIPASNHTYTPDFLLPNGIFVETKGLWESDDRKKHLLIREQHPELDIRIVFSSSRTKLYKGSPTSYGEFCEKHGIKFADKLIPAEWIKEPKKEVPFDRLKRK 145
               SCOP domains d2pfjb_ B: automated matches                                                                                                       SCOP domains
               CATH domains 2pfjB00 B:16-145  [code=3.40.91.30, no name defined]                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.....ee..eeeeeee..eeeee...ee.............hhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhh..eee...hhhhhhh.....hhhhhee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pfj B  16 RSGLEDKVSKQLESKGIKFEYEEWKVPYVIPASNHTYTPDFLLPNGIFVETAGLWESDDRKKHLLIREQHPELDIRIVFSSSRTKLYKGSPTSYGEFCEKHGIKFADKLIPAEWIKEPKKEVPFDRLKRK 145
                                    25        35        45        55        65        75        85        95       105       115       125       135       145


Chain Y from PDB  Type:DNA  Length:27
                                                           
                 2pfj Y   1 AGTTGAGTCCTTGTCAAGGGGCTGCTA  29
                                    10   ||   22       
                                        14|            
                                         17            


Chain Z from PDB  Type:DNA  Length:27
                                                           
                 2pfj Z   1 TAGCAGCCTGAGCTGCTCAACTCAACT  29
                                    10   ||   22       
                                        14|            
                                         17
   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  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ENDO_BPT7 | P00641)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008833    deoxyribonuclease IV (phage-T4-induced) activity    Catalysis of the endonucleolytic cleavage to 5'-phosphooligonucleotide end-products.
    GO:0004536    deoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0039657    suppression by virus of host gene expression    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ENDO_BPT7 | P00641: 1fzr 1m0d 1m0i 3cae

(-) Related Entries Specified in the PDB File

1fzr CRYSTAL STRUCTURE OF BACTERIOPHAGE T7 ENDONUCLEASE I
1m0d CRYSTAL STRUCTURE OF BACTERIOPHAGE T7 ENDONUCLEASE I WITH A WILD-TYPE ACTIVE SITE AND BOUND MANGANESE IONS
1m0i CRYSTAL STRUCTURE OF BACTERIOPHAGE T7 ENDONUCLEASE I WITH A WILD-TYPE ACTIVE SITE