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(-) Description

Title :  CRYSTAL STRUCTURE OF BACTERIOPHAGE T7 ENDONUCLEASE I WITH A WILD-TYPE ACTIVE SITE
 
Authors :  J. M. Hadden, A. C. Declais, S. E. Phillips, D. M. Lilley
Date :  13 Jun 02  (Deposition) - 18 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Holliday Junction Resolvase, Homodimer, Domain Swapped, Composite Active Site, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Hadden, A. C. Declais, S. E. Phillips, D. M. Lilley
Metal Ions Bound At The Active Site Of The Junction-Resolving Enzyme T7 Endonuclease I
Embo J. V. 21 3505 2002
PubMed-ID: 12093751  |  Reference-DOI: 10.1093/EMBOJ/CDF337
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDODEOXYRIBONUCLEASE I
    Chains: A, B, C, D
    EC Number: 3.1.21.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET 19B
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 12-149
    Gene: ENDONUCLEASE I
    Organism Scientific: ENTEROBACTERIA PHAGE T7
    Organism Taxid: 10760
    Synonym: ENDONUCLEASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:66 , LYS A:67 , SER B:17 , LEU B:19 , GLU B:20 , HOH B:1012BINDING SITE FOR RESIDUE SO4 B 1001
2AC2SOFTWARESER A:17 , GLU A:20 , THR B:66 , GLY B:68BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWARESER C:17 , THR D:66 , GLY D:68 , HOH D:166BINDING SITE FOR RESIDUE SO4 C 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M0I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M0I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M0I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M0I)

(-) Exons   (0, 0)

(no "Exon" information available for 1M0I)

(-) 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: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 d1m0ia_ A: Endonuclease I (Holliday junction resolvase)                                                                           SCOP domains
               CATH domains 1m0iA00 A:17-145  [code=3.40.91.30, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....ee..eeeeeee..eeeee...ee.....eeeee...hhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhh..eee...hhhhhh......hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m0i A  17 SGLEDKVSKQLESKGIKFEYEEWKVPYVIPASNHTYTPDFLLPNGIFVETKGLWESDDRKKHLLIREQHPELDIRIVFSSSRTKLYKGSPTSYGEFCEKHGIKFADKLIPAEWIKEPKKEVPFDRLKRK 145
                                    26        36        46        56        66        76        86        96       106       116       126       136         


Chain B 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 d1m0ib_ B: Endonuclease I (Holliday junction resolvase)                                                                           SCOP domains
               CATH domains 1m0iB00 B:17-145  [code=3.40.91.30, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....ee....eeeee..eeeee...ee....eeeeee...hhhhhhhhhhhhhhh...eeeeee.............hhhhhhhhhh..eee...hhhhhh......hhhhhee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m0i B  17 SGLEDKVSKQLESKGIKFEYEEWKVPYVIPASNHTYTPDFLLPNGIFVETKGLWESDDRKKHLLIREQHPELDIRIVFSSSRTKLYKGSPTSYGEFCEKHGIKFADKLIPAEWIKEPKKEVPFDRLKRK 145
                                    26        36        46        56        66        76        86        96       106       116       126       136         


Chain C 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 d1m0ic_ C: Endonuclease I (Holliday junction resolvase)                                                                           SCOP domains
               CATH domains 1m0iC00 C:17-145  [code=3.40.91.30, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....ee..eeeeeee..eeeee...ee.....eeeee...hhhhhhhhhhhhhhh....eeeee.............hhhhhhhhh..eeee...hhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m0i C  17 SGLEDKVSKQLESKGIKFEYEEWKVPYVIPASNHTYTPDFLLPNGIFVETKGLWESDDRKKHLLIREQHPELDIRIVFSSSRTKLYKGSPTSYGEFCEKHGIKFADKLIPAEWIKEPKKEVPFDRLKRK 145
                                    26        36        46        56        66        76        86        96       106       116       126       136         


Chain D 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 d1m0id_ D: Endonuclease I (Holliday junction resolvase)                                                                           SCOP domains
               CATH domains 1m0iD00 D:17-145  [code=3.40.91.30, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..........eeeee..eeeee...ee.....eeeee...hhhhhhhhhhhhhhh....eeeee.............hhhhhhhhh...eee...hhhhhh......hhhhhee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m0i D  17 SGLEDKVSKQLESKGIKFEYEEWKVPYVIPASNHTYTPDFLLPNGIFVETKGLWESDDRKKHLLIREQHPELDIRIVFSSSRTKLYKGSPTSYGEFCEKHGIKFADKLIPAEWIKEPKKEVPFDRLKRK 145
                                    26        36        46        56        66        76        86        96       106       116       126       136
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1M0I)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  3.1.21.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENDO_BPT7 | P00641: 1fzr 1m0d 2pfj 3cae

(-) Related Entries Specified in the PDB File

1fzr BACTERIOPHAGE T7 ENDONUCLEASE I E65K MUTANT
1m0d BACTERIOPHAGE T7 ENDONUCLEASE I