Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF A NEW MAGNESIUM ION BINDING SITE NEAR TYR94 IN THE RESTRICTION ENDONUCLEASE PVUII
 
Authors :  A. Spyridaki, C. Matzen, T. Lanio, A. Jeltsch, A. Simoncsits, A. Athanasiadis, E. Scheuring-Vanamee, M. Kokkinidis, A. Pingoud
Date :  20 May 01  (Deposition) - 07 Aug 03  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Endonuclease, Type Ii Restriction Endonuclease, Hydrolase, Nuclease, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Spyridaki, C. Matzen, T. Lanio, A. Jeltsch, A. Simoncsits, A. Athanasiadis, E. Scheuring-Vanamee, M. Kokkinidis, A. Pingoud
Structural And Biochemical Characterization Of A New Mg(2+) Binding Site Near Tyr94 In The Restriction Endonuclease Pvuii.
J. Mol. Biol. V. 331 395 2003
PubMed-ID: 12888347  |  Reference-DOI: 10.1016/S0022-2836(03)00692-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYPE II RESTRICTION ENZYME PVUII
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPVU1
    Expression System Strain: HB101
    Expression System Taxid: 634468
    Expression System Vector: PPUC18
    Organism Scientific: PROTEUS VULGARIS
    Organism Taxid: 585
    Synonym: ENDONUCLEASE PVUII, R.PVUII

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:58 , GLU A:68 , LYS A:70 , HOH A:2014 , HOH A:2016BINDING SITE FOR RESIDUE MG A 1
2AC2SOFTWARETHR B:82 , HIS B:83 , TYR B:94 , HOH B:2013BINDING SITE FOR RESIDUE MG B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H56)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H56)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H56)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H56)

(-) Exons   (0, 0)

(no "Exon" information available for 1H56)

(-) 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 d1h56a_ A: Restriction endonuclease PvuII                                                                                                                    SCOP domains
               CATH domains 1h56A00 A:2-157 PVUII Endonuclease, subunit A                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.ee........ee.......eeeeee.....ee......hhhhhhhhh...eeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhhh.........eehhhhhhhheeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h56 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: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 d1h56b_ B: Restriction endonuclease PvuII                                                                                                                    SCOP domains
               CATH domains 1h56B00 B:2-157 PVUII Endonuclease, subunit A                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.ee........ee.....eeeeeeee.....ee......hhhhhhhhhh..eeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhhh.........eehhhhhhhheeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h56 B   2 SHPDLNKLLELWPHIQEYQDLALKHGINDIFQDNGGKLLQVLLITGLTVLPGREGNDAVDNAGQEYELKSINIDLTKGFSTHHHMNPVIIAKYRQVPWIFAIYRGIAIEAIYRLEPKDLEFYYDKWERKWYSDGHKDINNPKIPVKYVMEHGTKIY 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
   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 1H56)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1h56)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1h56
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  T2P2_PROHU | P23657
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.21.4
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  T2P2_PROHU | P23657
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1eyu HIGH RESOLUTION STRUCTURE OF THE PVUII ENDONCULEASE/COGNATE DNA COMPLEX AT PH 4.6
1f0o PVUII ENDONUCLEASE/COGNATE DNA COMPLEX ( GLUTARALDEHYDE-CROSSLINKED CRYSTAL) AT PH 7. 5 WITH TWO CALCIUM IONS ATEACH ACTIVE SITE
1k0z CRYSTAL STRUCTURE OF THE PVUII ENDONUCLEASE WITH PR3+ ANDSO4 IONS BOUND IN THE ACTIVE SITE AT 2.05A.
1ni0 STRUCTURE OF THE Y94F MUTANT OF THE RESTRICTIONENDONUCLEASE PVUII
1pvi PVUII ENDONUCLEASE COMPLEXED WITH COGNATE DEOXYRIBONUCLEIC ACID
1pvu PVUII RESTRICTION ENDONUCLEASE
2pvi PVUII ENDONUCLEASE COMPLEXED TO AN IODINATED COGNATE DEOXYRIBONUCLEIC ACID
3pvi D34G MUTANT OF PVUII ENDONUCLEASE COMPLEXED WITH COGNATE DEOXYRIBONUCLEIC ACID SHOWS THAT ASP34 IS DIRECTLY INVOLVED IN DEOXYRIBONUCLEIC ACID RECOGNITION AND INDIRECTLY INVOLVED IN CATALYSIS