Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF TETRAMERIC RESTRICTION ENDONUCLEASE SFII BOUND TO COGNATE DNA.
 
Authors :  A. K. Aggarwal, E. S. Vanamee, H Viadiu
Date :  10 Nov 05  (Deposition) - 24 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,F,G
Biol. Unit 1:  A,B,F,G  (2x)
Keywords :  Type Iif Restriction Endonuclease, Protein/Dna Complex, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. S. Vanamee, H. Viadiu, R. Kucera, L. Dorner, S. Picone, I. Schildkraut, A. K. Aggarwal
A View Of Consecutive Binding Events From Structures Of Tetrameric Endonuclease Sfii Bound To Dna
Embo J. V. 24 4198 2005
PubMed-ID: 16308566  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600880
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*T)-3'
    Chains: F
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'- D(*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*A)-3'
    Chains: G
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - TYPE II RESTRICTION ENZYME SFII
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Other Details: E. COLI
    Synonym: ENDONUCLEASE SFII, R.SFII
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABFG
Biological Unit 1 (2x): ABFG

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:79 , ASP A:100 , ALA A:101BINDING SITE FOR RESIDUE CA A 270
2AC2SOFTWAREASP B:79 , ASP B:100 , ALA B:101BINDING SITE FOR RESIDUE CA B 270

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2EZV)

(-) 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:267
 aligned with T2S1_STRFI | O52512 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:269
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         
           T2S1_STRFI     1 MHQDYRELSLDELESVEKQTLRTIVQALQQYSKEAKSIFETTAADSSGEVIVLAEDITQYALEVAETYPINRRFAGFIDYKRVRWLPSPHGLLPQVLLVDAKASTEKNRDTLQRSQLPMDAEFRNTSSGEVVTMEAGVIPHLMLQSANDGVLPAVTTSIFVHFYYRELKDVEGRYRELKSIYVLSLPHARLKQRYNPDPDTSFFGAGKHSPARGEVARIRVYFDRLKEACPWRLQELHYSADSEYTQPRWRDLNDAGHEVTKEFLFLER 269
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh................eeeeeee......eeeeeeeeeeee.....eeehhhhh...eeee......eeee......eeeee.....eeeeeeeeeeeeeeeee..--....eeeeeeeeeee.hhhhhhhhh.......eee............eeehhhhhhhhh...eeeee..........eeeee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ezv A   1 MHQDYRELSLDELESVEKQTLRTIVQALQQYSKEAKSIFETTAADSSGEVIVLAEDITQYALEVAETYPINRRFAGFIDYKRVRWLPSPHGLLPQVLLVDAKASTEKNRDTLQRSQLPMDAEFRNTSSGEVVTMEAGVIPHLMLQSANDGVLPAVTTSIFVHFYYRELK--EGRYRELKSIYVLSLPHARLKQRYNPDPDTSFFGAGKHSPARGEVARIRVYFDRLKEACPWRLQELHYSADSEYTQPRWRDLNDAGHEVTKEFLFLER 269
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        |- |     180       190       200       210       220       230       240       250       260         
                                                                                                                                                                                                  169  |                                                                                                 
                                                                                                                                                                                                     172                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:269
 aligned with T2S1_STRFI | O52512 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:269
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         
           T2S1_STRFI     1 MHQDYRELSLDELESVEKQTLRTIVQALQQYSKEAKSIFETTAADSSGEVIVLAEDITQYALEVAETYPINRRFAGFIDYKRVRWLPSPHGLLPQVLLVDAKASTEKNRDTLQRSQLPMDAEFRNTSSGEVVTMEAGVIPHLMLQSANDGVLPAVTTSIFVHFYYRELKDVEGRYRELKSIYVLSLPHARLKQRYNPDPDTSFFGAGKHSPARGEVARIRVYFDRLKEACPWRLQELHYSADSEYTQPRWRDLNDAGHEVTKEFLFLER 269
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.............eeeeeee......eeeeeeeeeeee.....eee........eeee......eeee......eeeee.....eeeeeeeeeeeeeeeee........eeeeeeeeeee.hhhhhhhhh.......eee............eeehhhhhhhhh...eeeee..........eeeee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ezv B   1 MHQDYRELSLDELESVEKQTLRTIVQALQQYSKEAKSIFETTAADSSGEVIVLAEDITQYALEVAETYPINRRFAGFIDYKRVRWLPSPHGLLPQVLLVDAKASTEKNRDTLQRSQLPMDAEFRNTSSGEVVTMEAGVIPHLMLQSANDGVLPAVTTSIFVHFYYRELKDVEGRYRELKSIYVLSLPHARLKQRYNPDPDTSFFGAGKHSPARGEVARIRVYFDRLKEACPWRLQELHYSADSEYTQPRWRDLNDAGHEVTKEFLFLER 269
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         


Chain F from PDB  Type:DNA  Length:15
                                               
                 2ezv F   4 TGGCCAACAAGGCCT  18
                                    13     


Chain G from PDB  Type:DNA  Length:15
                                               
                 2ezv G  24 AGGCCTTGTTGGCCA  38
                                    33
   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  (0, 0)

(no "SCOP Domain" information available for 2EZV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2EZV)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (T2S1_STRFI | O52512)
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: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 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ezv)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  2ezv
    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
  T2S1_STRFI | O52512
    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
  T2S1_STRFI | O52512
    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
        T2S1_STRFI | O52512: 2f03

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2EZV)