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(-) Description

Title :  STRUCTURE OF RESTRICTION ENDONUCLEASE FOKI
 
Authors :  D. A. Wah, J. Bitinaite, I. Schildkraut, A. K. Aggarwal
Date :  30 Mar 98  (Deposition) - 17 Jun 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nucleic Acid Recognition, Dna-Binding Protein, Type Iis Restriction Endonuclease, Deoxyribonuclease, Dna Hydrolysis, Dna Cleavage, Metalloenzyme, Metal Ion Catalysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Wah, J. Bitinaite, I. Schildkraut, A. K. Aggarwal
Structure Of Foki Has Implications For Dna Cleavage.
Proc. Natl. Acad. Sci. Usa V. 95 10564 1998
PubMed-ID: 9724743  |  Reference-DOI: 10.1073/PNAS.95.18.10564
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FOKI RESTRICTION ENDONUCLEASE
    Atcc: ATCC 33414
    Chains: A, B
    Collection: ATCC 33414
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: FULL-LENGTH
    Gene: FOKI
    Organism Scientific: PLANOMICROBIUM OKEANOKOITES
    Organism Taxid: 244
    Strain: IFO12536
    Synonym: R.FOKI

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2FOK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FOK)

(-) 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:558
 aligned with T2F1_PLAOK | P14870 from UniProtKB/Swiss-Prot  Length:583

    Alignment length:575
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578     
           T2F1_PLAOK     9 IRTFGWVQNPGKFENLKRVVQVFDRNSKVHNEVKNIKIPTLVKESKIQKELVAIMNQHDLIYTYKELVGTGTSIRSEAPCDAIIQATIADQGNKKGYIDNWSSDGFLRWAHALGFIEYINKSDSFVITDVGLAYSKSADGSAIEKEILIEAISSYPPAIRILTLLEDGQHLTKFDLGKNLGFSGESGFTSLPEGILLDTLANAMPKDKGEIRNNWEGSSDKYARMIGGWLDKLGLVKQGKKEFIIPTLGKPDNKEFISHAFKITGEGLKVLRRAKGSTKFTRVPKRVYWEMLATNLTDKEYVRTRRALILEILIKAGSLKIEQIQDNLKKLGFDEVIETIENDIKGLINTGIFIEIKGRFYQLKDHILQFVIPNRGVTKQLVKSELEEKKSELRHKLKYVPHEYIELIEIARNSTQDRILEMKVMEFFMKVYGYRGKHLGGSRKPDGAIYTVGSPIDYGVIVDTKAYSGGYNLPIGQADEMQRYVEENQTRNKHINPNEWWKVYPSSVTEFKFLFVSGHFKGNYKAQLTRLNHITNCNGAVLSVEELLIGGEMIKAGTLTLEEVRRKFNNGEINF 583
               SCOP domains d2foka1 A:5-143 Restriction endonuclease FokI, N-terminal (recognition)      domain                                                        d2foka2 A:144-286 Restriction endonuclease FokI, N-terminal (recognition) domain                                                               d2foka3 A:287-386 Restriction endonuclease FokI, N-terminal (recognition) domain                    d2foka4 A:387-579 Restriction endonuclease FokI, C-terminal (catalytic) domain                                                                                                                    SCOP domains
               CATH domains 2fokA01 A:5-292 Foki Restriction Endonuclease, Chain A, domain 1                                                                                                                                                                                                                                ---------2fokA02 A:302-388 'winged helix' repressor DNA binding domain                          ------------2fokA03 A:401-575  [code=3.40.91.30, no name defined]                                                                                                                          ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhh.....hhhhhhhh.hhhhh...hhhhhhhhhhhh.......hhhhh....-----.....hhhhh.....--.......hhhhhhhhhhh...eeee....eeee.hhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhh.......hhhhhhh.............hhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhh...eee..eeee...-----.eeee...eee.hhhhhhhhhhh.............hhh.......hhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhh...eeee..eeee............-----....hhhhhhhhhh.......hhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eeee........eeee........eeeeeee.........hhhhhhhhhhhhhhhh.........hhhh.......eeeeeee......hhhhhhhhhhhh..eeeeeehhhhhhhhhhhhh....hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fok A   5 IRTFGWVQNPGKFENLKRVVQVFDRNSKVHNEVKNIKIPTLVKESKIQKELVAIMNQHDLIYTYKELVGTGT-----APCDAIIQATIADQG--KGYIDNWSSDGFLRWAHALGFIEYINKSDSFVITDVGLAYSKSADGSAIEKEILIEAISSYPPAIRILTLLEDGQHLTKFDLGKNLGFSGESGFTSLPEGILLDTLANAMPKDKGEIRNNWEGSSDKYARMIGGWLDKLGLVKQGKKEFIIPT-----NKEFISHAFKITGEGLKVLRRAKGSTKFTRVPKRVYWEMLATNLTDKEYVRTRRALILEILIKAGSLKIEQIQDNLKKLGFDEVIETIENDIKGLINTGIFIEIKGRFYQLKDHILQFVIPNR-----LVKSELEEKKSELRHKLKYVPHEYIELIEIARNSTQDRILEMKVMEFFMKVYGYRGKHLGGSRKPDGAIYTVGSPIDYGVIVDTKAYSGGYNLPIGQADEMQRYVEENQTRNKHINPNEWWKVYPSSVTEFKFLFVSGHFKGNYKAQLTRLNHITNCNGAVLSVEELLIGGEMIKAGTLTLEEVRRKFNNGEINF 579
                                    14        24        34        44        54        64        74 |     |84        94 |  |  104       114       124       134       144       154       164       174       184       194       204       214       224       234       244      |  -  |    264       274       284       294       304       314       324       334       344       354       364       374    |    -|      394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574     
                                                                                                  76    82            96 99                                                                                                                                                     251   257                                                                                                                       379   385                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:560
 aligned with T2F1_PLAOK | P14870 from UniProtKB/Swiss-Prot  Length:583

    Alignment length:575
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578     
           T2F1_PLAOK     9 IRTFGWVQNPGKFENLKRVVQVFDRNSKVHNEVKNIKIPTLVKESKIQKELVAIMNQHDLIYTYKELVGTGTSIRSEAPCDAIIQATIADQGNKKGYIDNWSSDGFLRWAHALGFIEYINKSDSFVITDVGLAYSKSADGSAIEKEILIEAISSYPPAIRILTLLEDGQHLTKFDLGKNLGFSGESGFTSLPEGILLDTLANAMPKDKGEIRNNWEGSSDKYARMIGGWLDKLGLVKQGKKEFIIPTLGKPDNKEFISHAFKITGEGLKVLRRAKGSTKFTRVPKRVYWEMLATNLTDKEYVRTRRALILEILIKAGSLKIEQIQDNLKKLGFDEVIETIENDIKGLINTGIFIEIKGRFYQLKDHILQFVIPNRGVTKQLVKSELEEKKSELRHKLKYVPHEYIELIEIARNSTQDRILEMKVMEFFMKVYGYRGKHLGGSRKPDGAIYTVGSPIDYGVIVDTKAYSGGYNLPIGQADEMQRYVEENQTRNKHINPNEWWKVYPSSVTEFKFLFVSGHFKGNYKAQLTRLNHITNCNGAVLSVEELLIGGEMIKAGTLTLEEVRRKFNNGEINF 583
               SCOP domains d2fokb1 B:5-143 Restriction endonuclease FokI, N-terminal   (recognition     ) domain                                                      d2fokb2 B:144-286 Restriction endonuclease FokI, N-terminal (recognition) domain                                                               d2fokb3 B:287-378 Restriction endonuclease FokI, N-terminal (recognition) domain                    d2fokb4 B:387-579 Restriction endonuclease FokI, C-terminal (catalytic) domain                                                                                                                    SCOP domains
               CATH domains 2fokB01 B:5-292 Foki Restriction Endonuclease, Chain A, d  omain 1                                                                                                                                                                                                                              ---------2fokB02 B:302-388 'winged helix' repressor DNA binding domain                          ------------2fokB03 B:401-576  [code=3.40.91.30, no name defined]                                                                                                                           --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhh....hhhhhhh...hhhh...hhhhhhhhhh...--....hhhhh....-----.....hhhhh...hhh......hhhhhhhhhhhhh...eeee....eeee.hhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhh.......hhhhhhh......hhh....hhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhh...eee..eeee.........eeee...eee.hhhhhhhhhhh.............hhh.......hhhhhhhhhhhhhhhh......hhhhhhhhhhh.....hhhhhhhhhhhhh....eeee..eeee...........--------..hhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhh....eeee........eeee........eeeeeee.........hhhhhhhhhhhhhhhh.........hhhh.......eeeeeee......hhhhhhhhhhhh..eeeeeehhhhhhhhhhhhh....hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fok B   5 IRTFGWVQNPGKFENLKRVVQVFDRNSKVHNEVKNIKIPTLVKESKIQKELVAIMNQ--LIYTYKELVGTGT-----APCDAIIQATIADQGNKKGYIDNWSSDGFLRWAHALGFIEYINKSDSFVITDVGLAYSKSADGSAIEKEILIEAISSYPPAIRILTLLEDGQHLTKFDLGKNLGFSGESGFTSLPEGILLDTLANAMPKDKGEIRNNWEGSSDKYARMIGGWLDKLGLVKQGKKEFIIPTLGKPDNKEFISHAFKITGEGLKVLRRAKGSTKFTRVPKRVYWEMLATNLTDKEYVRTRRALILEILIKAGSLKIEQIQDNLKKLGFDEVIETIENDIKGLINTGIFIEIKGRFYQLKDHILQFVIPN--------KSELEEKKSELRHKLKYVPHEYIELIEIARNSTQDRILEMKVMEFFMKVYGYRGKHLGGSRKPDGAIYTVGSPIDYGVIVDTKAYSGGYNLPIGQADEMQRYVEENQTRNKHINPNEWWKVYPSSVTEFKFLFVSGHFKGNYKAQLTRLNHITNCNGAVLSVEELLIGGEMIKAGTLTLEEVRRKFNNGEINF 579
                                    14        24        34        44        54      | 64        74 |     |84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374   |     -  |    394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574     
                                                                                   61 64          76    82                                                                                                                                                                                                                                                                                                     378      387
   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  (2, 8)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (T2F1_PLAOK | P14870)
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:0004536    deoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
    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.

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 Databases and Analysis Tools

(-) Databases

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  2fok
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  3.1.21.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        T2F1_PLAOK | P14870: 1fok

(-) Related Entries Specified in the PDB File

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