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(-) Description

Title :  ENDONUCLEASE VII (ENDOVII) FROM PHAGE T4
 
Authors :  H. Raaijmakers, O. Vix, I. Toro, D. Suck
Date :  07 Feb 99  (Deposition) - 07 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Endonuclease, Resolvase, Holliday Junction, Dnase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Raaijmakers, O. Vix, I. Toro, S. Golz, B. Kemper, D. Suck
X-Ray Structure Of T4 Endonuclease Vii: A Dna Junction Resolvase With A Novel Fold And Unusual Domain-Swapped Dimer Architecture.
Embo J. V. 18 1447 1999
PubMed-ID: 10075917  |  Reference-DOI: 10.1093/EMBOJ/18.6.1447
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RECOMBINATION ENDONUCLEASE VII
    Chains: A, B
    EC Number: 3.1.22.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Cellular Location: CYTOPLASM
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: GP49
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Other Details: ONE ZN BOUND TO CYS 23,26,58,61 OF EACH CHAIN CA LIGANDED TO ASP40 AND ASN 62
    Synonym: PROTEIN GP49

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:23 , CYS A:26 , CYS A:58 , CYS A:61BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWARECYS B:23 , CYS B:26 , CYS B:58 , CYS B:61BINDING SITE FOR RESIDUE ZN B 402
3AC3SOFTWAREHIS A:38 , ASP A:40 , ASN A:62 , HOH A:447 , HOH A:450BINDING SITE FOR RESIDUE CA A 403
4AC4SOFTWAREGLU B:29 , ASP B:40 , ASN B:62 , HOH B:444BINDING SITE FOR RESIDUE CA B 404
5AC5SOFTWAREASP A:17 , ASN A:20 , GLY B:81 , GLU B:86 , HOH B:448BINDING SITE FOR RESIDUE CA B 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EN7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1EN7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EN7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EN7)

(-) Exons   (0, 0)

(no "Exon" information available for 1EN7)

(-) 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:157
 aligned with END7_BPT4 | P13340 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
            END7_BPT4     1 MLLTGKLYKEEKQKFYDAQNGKCLICQRELNPDVQANHLDHDHELNGPKAGKVRGLLCNLCNAAEGQMKHKFNRSGLKGQGVDYLEWLENLLTYLKSDYTQNNIHPNFVGDKSKEFSRLGKEEMMAEMLQRGFEYNESDTKTQLIASFKKQLRKSLK 157
               SCOP domains d1en7a2 A:1-103 Recombination endonuclease VII, N-terminal domain                                      d1en7a1 A:104-157                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------1en7A02 A:103-157  [code=1.10.720.10, no name defined]  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh...............hhh.eeee...........eeeee.hhhhhhhhhhhhhhhhh..hhh...hhhhhhhhhhhhh.........hhhhhhhhhhhhh..hhhhhhhhh...........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1en7 A   1 MLLTGKLYKEEKQKFYDAQNGKCLICQRELNPDVQANHLDHDHELNGPKAGKVRGLLCNLCNAAEGQMKHKFNRSGLKGQGVDYLEWLENLLTYLKSDYTQNNIHPNFVGDKSKEFSRLGKEEMMAEMLQRGFEYNESDTKTQLIASFKKQLRKSLK 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with END7_BPT4 | P13340 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
            END7_BPT4     1 MLLTGKLYKEEKQKFYDAQNGKCLICQRELNPDVQANHLDHDHELNGPKAGKVRGLLCNLCNAAEGQMKHKFNRSGLKGQGVDYLEWLENLLTYLKSDYTQNNIHPNFVGDKSKEFSRLGKEEMMAEMLQRGFEYNESDTKTQLIASFKKQLRKSLK 157
               SCOP domains d1en7b2 B:1-103 Recombination endonuclease VII, N-terminal domain                                      d1en7b1 B:104-157                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------1en7B02 B:103-157  [code=1.10.720.10, no name defined]  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh...............hhh.eeee...........eeeee.hhhhhhhhhhhhhhhhh.hhhh...hhhhhhhhhhhh..........hhhhhhhhhhhhh..hhhhhhhhhh..........hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1en7 B   1 MLLTGKLYKEEKQKFYDAQNGKCLICQRELNPDVQANHLDHDHELNGPKAGKVRGLLCNLCNAAEGQMKHKFNRSGLKGQGVDYLEWLENLLTYLKSDYTQNNIHPNFVGDKSKEFSRLGKEEMMAEMLQRGFEYNESDTKTQLIASFKKQLRKSLK 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EN7)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (END7_BPT4 | P13340)
molecular function
    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.
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.

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 Related Entries

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UniProtKB/Swiss-Prot
        END7_BPT4 | P13340: 1e7d 1e7l 2qnc 2qnf

(-) Related Entries Specified in the PDB File

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