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

(-) Description

Title :  DNA BINDING DOMAIN OF RESTRICTION ENDONUCLEASE BOUND TO DNA
 
Authors :  R. Sukackaite, S. Grazulis, V. Siksnys
Date :  08 Jul 11  (Deposition) - 23 May 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Restriction Endonuclease, 5-Methylcytosine, Base Flipping, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Sukackaite, S. Grazulis, G. Tamulaitis, V. Siksnys
The Recognition Domain Of The Methyl-Specific Endonuclease Mcrbc Flips Out 5-Methylcytosine.
Nucleic Acids Res. V. 40 7552 2012
PubMed-ID: 22570415  |  Reference-DOI: 10.1093/NAR/GKS332

(-) Compounds

Molecule 1 - 5-METHYLCYTOSINE-SPECIFIC RESTRICTION ENZYME B
    Chains: A, B
    EC Number: 3.1.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD24
    Expression System Strain: ER2267
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DNA BINDING DOMAIN
    Gene: MCRB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: ECOKMCRBC
 
Molecule 2 - DNA (5'-D(*T*GP*AP*GP*AP*(5CM)P*CP*GP*GP*TP*AP*GP*C)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*A*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*TP*C)-3')
    Chains: D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
15CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 3SSD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SSD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SSD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SSD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SSD)

(-) Exons   (0, 0)

(no "Exon" information available for 3SSD)

(-) 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:155
 aligned with MCRB_ECOLI | P15005 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     
           MCRB_ECOLI     2 ESIQPWIEKFIKQAQQQRSQSTKDYPTSYRNLRVKLSFGYGNFTSIPWFAFLGEGQEASNGIYPVILYYKDFDELVLAYGISDTNEPHAQWQFSSDIPKTIAEYFQATSGVYPKKYGQSYYACSQKVSQGIDYTRFASMLDNIINDYKLIFNSGK 156
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..........ee..eeeeeeee...eeeeeeeeee.........eeeeeeeehhh.eeeeeeee..................hhhhhhhhhhh.........eeeeeee.hhh.hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ssd A   2 ESIQPWIEKFIKQAQQQRSQSTKDYPTSYRNLRVKLSFGYGNFTSIPWFAFLGEGQEASNGIYPVILYYKDFDELVLAYGISDTNEPHAQWQFSSDIPKTIAEYFQATSGVYPKKYGQSYYACSQKVSQGIDYTRFASMLDNIINDYKLIFNSGK 156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     


Chain B from PDB  Type:PROTEIN  Length:148
 aligned with MCRB_ECOLI | P15005 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        
           MCRB_ECOLI     3 SIQPWIEKFIKQAQQQRSQSTKDYPTSYRNLRVKLSFGYGNFTSIPWFAFLGEGQEASNGIYPVILYYKDFDELVLAYGISDTNEPHAQWQFSSDIPKTIAEYFQATSGVYPKKYGQSYYACSQKVSQGIDYTRFASMLDNIINDYKL 150
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh..........ee..eeeeee..........eeeee.........eeeeeeeehhh.eeeeeeee..................hhhhhhhhhh..........eeeeeee.hhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ssd B   3 SIQPWIEKFIKQAQQQRSQSTKDYPTSYRNLRVKLSFGYGNFTSIPWFAFLGEGQEASNGIYPVILYYKDFDELVLAYGISDTNEPHAQWQFSSDIPKTIAEYFQATSGVYPKKYGQSYYACSQKVSQGIDYTRFASMLDNIINDYKL 150
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        


Chain C from PDB  Type:DNA  Length:12
                                            
                 3ssd C   2 GAGAcCGGTAGC  13
                                |   11  
                                6-5CM   


Chain D from PDB  Type:DNA  Length:12
                                            
                 3ssd D   2 GCTACCGGTCTC  13
                                    11
   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 3SSD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SSD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SSD)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MCRB_ECOLI | P15005)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    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.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0015666    restriction endodeoxyribonuclease activity    Catalysis of endonucleolytic cleavage of DNA in a site-specific manner, resulting in double-strand breaks.
biological process
    GO:0006308    DNA catabolic process    The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    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
    5CM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3ssd)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ssd)
 

(-) 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 ](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
  3ssd
    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
  MCRB_ECOLI | P15005
    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.-
    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
  MCRB_ECOLI | P15005
    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
        MCRB_ECOLI | P15005: 3ssc 3sse

(-) Related Entries Specified in the PDB File

3ssc 3sse