Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  METAL-DEPLETED ECL18KI IN COMPLEX WITH UNCLEAVED DNA
 
Authors :  M. Bochtler, R. H. Szczepanowski, G. Tamulaitis, S. Grazulis, H. Czapi E. Manakova, V. Siksnys
Date :  18 Jan 06  (Deposition) - 20 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
Keywords :  Ecl18Ki-Dna Complex, Type Ii Restriction Endonuclease, Nucleotide Flipping, Base Extrusion, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Bochtler, R. H. Szczepanowski, G. Tamulaitis, S. Grazulis, H. Czapinska, E. Manakova, V. Siksnys
Nucleotide Flips Determine The Specificity Of The Ecl18Ki Restriction Endonuclease
Embo J. V. 25 2219 2006
PubMed-ID: 16628220  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601096
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA STRAND 1
    ChainsE, G
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA STRAND 2
    ChainsF, H
    EngineeredYES
    SyntheticYES
 
Molecule 3 - R.ECL18KI
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUC129
    Expression System StrainJM109
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneECL18KIR
    Organism ScientificENTEROBACTER CLOACAE
    Organism Taxid550
    SynonymRESTRICTION ENDONUCLEASE

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)AB  EF  
Biological Unit 2 (1x)  CD  GH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2FQZ)

(-) Sites  (0, 0)

(no "Site" information available for 2FQZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Met A:163 -Pro A:164
2Met B:163 -Pro B:164
3Met C:163 -Pro C:164
4Met D:163 -Pro D:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FQZ)

(-) 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:290
 aligned with O87963_ENTCL | O87963 from UniProtKB/TrEMBL  Length:305

    Alignment length:299
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293         
         O87963_ENTCL     4 LSPGEFKTLISKERKSHFITPFALVYKTFCDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFFQKNQIGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATLDDSFSEETINILYEANVVVVTTVENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYTDSEKEEIQRSILKQIEKYSDFPYVVNYYRNRLSA 302
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhh---------......eee.hhhhhhhh....eeeeee....hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhh.eeeeehhhhhhhhh.....eeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fqz A   4 LSPGEFKTLISKERKSHFITPFALVYKTFCDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAI---------IGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATLDDSFSEETINILYEANVVVVTTVENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYTDSEKEEIQQSILKQIEKYSDFPYVVNYYRNRLSA 302
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143 |       - |     163       173       183       193       203       213       223       233       243       253       263       273       283       293         
                                                                                                                                                                       145       155                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:293
 aligned with O87963_ENTCL | O87963 from UniProtKB/TrEMBL  Length:305

    Alignment length:302
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303  
         O87963_ENTCL     4 LSPGEFKTLISKERKSHFITPFALVYKTFCDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFFQKNQIGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATLDDSFSEETINILYEANVVVVTTVENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYTDSEKEEIQRSILKQIEKYSDFPYVVNYYRNRLSALFD 305
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee....---------......eee.hhhhhhhh....eeeee.....hhhhhhhhhhhhhh...eeee......hhhhhhhhhhh.eeeeehhhhhhhhh.....eeehhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fqz B   4 LSPGEFKTLISKERKSHFITPFALVYKTFCDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAI---------IGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATLDDSFSEETINILYEANVVVVTTVENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYTDSEKEEIQQSILKQIEKYSDFPYVVNYYRNRLSALFD 305
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143 |       - |     163       173       183       193       203       213       223       233       243       253       263       273       283       293       303  
                                                                                                                                                                       145       155                                                                                                                                                      

Chain C from PDB  Type:PROTEIN  Length:292
 aligned with O87963_ENTCL | O87963 from UniProtKB/TrEMBL  Length:305

    Alignment length:301
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303 
         O87963_ENTCL     4 LSPGEFKTLISKERKSHFITPFALVYKTFCDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFFQKNQIGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATLDDSFSEETINILYEANVVVVTTVENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYTDSEKEEIQRSILKQIEKYSDFPYVVNYYRNRLSALF 304
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhh---------......eee.hhhhhhhh....eeeeee....hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhh.eeeeehhhhhhhhh......eehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fqz C   4 LSPGEFKTLISKERKSHFITPFALVYKTFCDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAI---------IGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATLDDSFSEETINILYEANVVVVTTVENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYTDSEKEEIQQSILKQIEKYSDFPYVVNYYRNRLSALF 304
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143 |       - |     163       173       183       193       203       213       223       233       243       253       263       273       283       293       303 
                                                                                                                                                                       145       155                                                                                                                                                     

Chain D from PDB  Type:PROTEIN  Length:292
 aligned with O87963_ENTCL | O87963 from UniProtKB/TrEMBL  Length:305

    Alignment length:301
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303 
         O87963_ENTCL     4 LSPGEFKTLISKERKSHFITPFALVYKTFCDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFFQKNQIGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATLDDSFSEETINILYEANVVVVTTVENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYTDSEKEEIQRSILKQIEKYSDFPYVVNYYRNRLSALF 304
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhh---------......eee.hhhhhhhh....eeeee.....hhhhhhhhhhhhhh...eeee......hhhhhhhhhhh.eeeeehhhhhhhhh.....eeehhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fqz D   4 LSPGEFKTLISKERKSHFITPFALVYKTFCDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAI---------IGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATLDDSFSEETINILYEANVVVVTTVENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYTDSEKEEIQQSILKQIEKYSDFPYVVNYYRNRLSALF 304
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143 |       - |     163       173       183       193       203       213       223       233       243       253       263       273       283       293       303 
                                                                                                                                                                       145       155                                                                                                                                                     

Chain E from PDB  Type:DNA  Length:9
                                         
                 2fqz E  -4 CGCCAGGGC   4

Chain F from PDB  Type:DNA  Length:9
                                         
                 2fqz F  -4 GCCCTGGCG   4

Chain G from PDB  Type:DNA  Length:9
                                         
                 2fqz G  -4 CGCCAGGGC   4

Chain H from PDB  Type:DNA  Length:9
                                         
                 2fqz H  -4 GCCCTGGCG   4

   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 2FQZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O87963_ENTCL | O87963)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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.
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
(no "Ligands, Modified Residues, Ions" information available for 2fqz)
 
  Sites
(no "Sites" information available for 2fqz)
 
  Cis Peptide Bonds
    Met A:163 - Pro A:164   [ RasMol ]  
    Met B:163 - Pro B:164   [ RasMol ]  
    Met C:163 - Pro C:164   [ RasMol ]  
    Met D:163 - Pro D:164   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2fqz
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  O87963_ENTCL | O87963
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  O87963_ENTCL | O87963
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O87963_ENTCL | O879632gb7

(-) Related Entries Specified in the PDB File

2gb7 SAME PROTEIN-DNA COMPLEX BUT THE IDENTITY OF NUCLEOTIDE (0) IN THE DNA CHAINS F AND H IS UNCERTAIN