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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF THE PVUII ENDONCULEASE/COGNATE DNA COMPLEX AT PH 4.6
 
Authors :  J. R. Horton, X. Cheng
Date :  09 May 00  (Deposition) - 21 Jul 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Endonuclease Type Ii, Restriction Enzyme, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Horton, X. Cheng
Pvuii Endonuclease Contains Two Calcium Ions In Active Sites.
J. Mol. Biol. V. 300 1049 2000
PubMed-ID: 10903853  |  Reference-DOI: 10.1006/JMBI.2000.3938
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3')
    Chains: C, D
    Engineered: YES
    Other Details: SELF-ANNEALING OLIGONUCLEOTIDE CONTAINING COGNATE SIX BASE PAIR SEQUENCE
    Synthetic: YES
 
Molecule 2 - TYPE II RESTRICTION ENZYME PVUII
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPR594
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PROTEUS VULGARIS
    Organism Taxid: 585
    Synonym: PVUII ENDONUCLEASE, R.PVUII

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1EYU)

(-) Sites  (0, 0)

(no "Site" information available for 1EYU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1EYU)

(-) 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:156
 aligned with T2P2_PROHU | P23657 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
           T2P2_PROHU     2 SHPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLPGREGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKYRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIY 157
               SCOP domains d1eyua_ A: Restriction endonuclease PvuII                                                                                                                    SCOP domains
               CATH domains 1eyuA00 A:2-157 PVUII Endonuclease, subunit A                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh..........eee.....eeeeeeee.....ee......hhhhhhhhhh..eeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhhh.........eehhhhhhhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1eyu A   2 SHPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLPGREGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKYRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIY 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      


Chain B from PDB  Type:PROTEIN  Length:153
 aligned with T2P2_PROHU | P23657 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
           T2P2_PROHU     2 SHPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLPGREGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKYRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIY 157
               SCOP domains d1eyub_ B: Restriction endonuclease PvuII                                                                                                                    SCOP domains
               CATH domains 1eyuB00 B:2-157 PVUII Endonuclease, subunit A                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.....---...ee.....eeeeeeee.....ee......hhhhhhhhhh..eeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhhh.........eehhhhhhhheeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1eyu B   2 SHPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLP---GNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKYRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIY 157
                                    11        21        31        41        51|   |   61        71        81        91       101       111       121       131       141       151      
                                                                             52  56                                                                                                     


Chain C from PDB  Type:DNA  Length:13
                                             
                 1eyu C   2 TGACCAGCTGGTC  14
                                    11   


Chain D from PDB  Type:DNA  Length:13
                                             
                 1eyu D   2 TGACCAGCTGGTC  14
                                    11
   Legend:   → Mismatch (orange background)
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  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 1EYU)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (T2P2_PROHU | P23657)
molecular function
    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: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:0009307    DNA restriction-modification system    A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
    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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  1eyu
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 Related Entries

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

UniProtKB/Swiss-Prot
        T2P2_PROHU | P23657: 1f0o 1h56 1k0z 1ni0 1pvi 1pvu 2pvi 3ksk 3pvi

(-) Related Entries Specified in the PDB File

1pvi 2pvi 3pvi