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(-) Description

Title :  THE CRYSTALLOGRAPHIC STRUCTURE OF RESTRICTION ENDONUCLEASE ECO RI AT 3.3 A IN THE ABSENSE OF DNA
 
Authors :  K. Chandrasekhar, M. M. Horvath, C. Samudzi, J. Choi, J. M. Rosenberg
Date :  18 May 99  (Deposition) - 10 Jun 99  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B (1x),C (1x)
Keywords :  Protein, Restriction Endonuclease, Apoenzyme, Endonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Chandrasekhar, M. M. Horvath, C. Samudzi, J. Choi, J. M. Rosenberg
The 3. 3 A Crystallographic Structure Of Restriction Endonuclease Eco Ri In The Absence Of Dna
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN (ECO RI ENDONUCLEASE)
    Chains: A, B, C
    EC Number: 3.1.21.4
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  B (1x)C (1x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1QC9)

(-) Sites  (0, 0)

(no "Site" information available for 1QC9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QC9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QC9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QC9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QC9)

(-) Exons   (0, 0)

(no "Exon" information available for 1QC9)

(-) 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:253
 aligned with T2E1_ECOLX | P00642 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:261
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276 
           T2E1_ECOLX    17 SQGVIGIFGDYAKAHDLAVGEVSKLVKKALSNEYPQLSFRYRDSIKKTEINEALKKIDPDLGGTLFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDIINIRNGLLVGKRGDQDLMAAGNAIERSHKNISEIANFMLSESHFPYVLFLEGSNFLTENISITRPDGRVVNLEYNSGILNRLDRLTAANYGMPINSNLCINKFVNHKDKSIMLQAASIYTQGDGREWDSKIMFEIMFDISTTSLRVLGRDLFEQLTSK 277
               SCOP domains d1qc9a_ A: Restriction endonuclease EcoRI                                                                                                                                                                                                                             SCOP domains
               CATH domains 1qc9A00 A:17-277 Eco RI Endonuclease, subunit A                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeee..eehhhhhhhhhhhh............ee...eeeeeee.....eeeeeeeeee........--------...........hhhhhhhhhhhhhhhhh.......eeeee.........ee.........ee...hhhhhhhhhhhhhhh..........................eeee.......hhhhhhhhhhhhhhhhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qc9 A  17 SQGVIGIFGDYAKAHDLAVGEVSKLVKKALSNEYPQLSFRYRDSIKKTEINEALKKIDPDLGGTLFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDIIN--------KRGDQDLMAAGNAIERSHKNISEIANFMLSESHFPYVLFLEGSNFLTENISITRPDGRVVNLEYNSGILNRLDRLTAANYGMPINSNLCINKFVNHKDKSIMLQAASIYTQGDGREWDSKIMFEIMFDISTTSLRVLGRDLFEQLTSK 277
                                    26        36        46        56        66        76        86        96       106       116    |    -   |   136       146       156       166       176       186       196       206       216       226       236       246       256       266       276 
                                                                                                                                  121      130                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:253
 aligned with T2E1_ECOLX | P00642 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:261
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276 
           T2E1_ECOLX    17 SQGVIGIFGDYAKAHDLAVGEVSKLVKKALSNEYPQLSFRYRDSIKKTEINEALKKIDPDLGGTLFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDIINIRNGLLVGKRGDQDLMAAGNAIERSHKNISEIANFMLSESHFPYVLFLEGSNFLTENISITRPDGRVVNLEYNSGILNRLDRLTAANYGMPINSNLCINKFVNHKDKSIMLQAASIYTQGDGREWDSKIMFEIMFDISTTSLRVLGRDLFEQLTSK 277
               SCOP domains d1qc9b_ B: Restriction endonuclease EcoRI                                                                                                                                                                                                                             SCOP domains
               CATH domains 1qc9B00 B:17-277 Eco RI Endonuclease, subunit A                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeee..eehhhhhhhhhhhh............ee...eeeeeee.....eeeeeeeeee........--------...........hhhhhhhhhhhhhhhhh.......eeeee.........ee.........ee...hhhhhhhhhhhhhhh..........................eeee.......hhhhhhhhhhhhhhhhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qc9 B  17 SQGVIGIFGDYAKAHDLAVGEVSKLVKKALSNEYPQLSFRYRDSIKKTEINEALKKIDPDLGGTLFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDIIN--------KRGDQDLMAAGNAIERSHKNISEIANFMLSESHFPYVLFLEGSNFLTENISITRPDGRVVNLEYNSGILNRLDRLTAANYGMPINSNLCINKFVNHKDKSIMLQAASIYTQGDGREWDSKIMFEIMFDISTTSLRVLGRDLFEQLTSK 277
                                    26        36        46        56        66        76        86        96       106       116    |    -   |   136       146       156       166       176       186       196       206       216       226       236       246       256       266       276 
                                                                                                                                  121      130                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:253
 aligned with T2E1_ECOLX | P00642 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:261
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276 
           T2E1_ECOLX    17 SQGVIGIFGDYAKAHDLAVGEVSKLVKKALSNEYPQLSFRYRDSIKKTEINEALKKIDPDLGGTLFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDIINIRNGLLVGKRGDQDLMAAGNAIERSHKNISEIANFMLSESHFPYVLFLEGSNFLTENISITRPDGRVVNLEYNSGILNRLDRLTAANYGMPINSNLCINKFVNHKDKSIMLQAASIYTQGDGREWDSKIMFEIMFDISTTSLRVLGRDLFEQLTSK 277
               SCOP domains d1qc9c_ C: Restriction endonuclease EcoRI                                                                                                                                                                                                                             SCOP domains
               CATH domains 1qc9C00 C:17-277 Eco RI Endonuclease, subunit A                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) EcoRI-1qc9C01 C:17-273                                                                                                                                                                                                                                           ---- Pfam domains (1)
           Pfam domains (2) EcoRI-1qc9C02 C:17-273                                                                                                                                                                                                                                           ---- Pfam domains (2)
           Pfam domains (3) EcoRI-1qc9C03 C:17-273                                                                                                                                                                                                                                           ---- Pfam domains (3)
         Sec.struct. author ..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeee..eehhhhhhhhhhhh............ee...eeeeeee.....eeeeeeeeee........--------...........hhhhhhhhhhhhhhhhh.......eeeee.........ee.........ee...hhhhhhhhhhhhhhh..........................eeee.......hhhhhhhhhhhhhhhhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qc9 C  17 SQGVIGIFGDYAKAHDLAVGEVSKLVKKALSNEYPQLSFRYRDSIKKTEINEALKKIDPDLGGTLFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDIIN--------KRGDQDLMAAGNAIERSHKNISEIANFMLSESHFPYVLFLEGSNFLTENISITRPDGRVVNLEYNSGILNRLDRLTAANYGMPINSNLCINKFVNHKDKSIMLQAASIYTQGDGREWDSKIMFEIMFDISTTSLRVLGRDLFEQLTSK 277
                                    26        36        46        56        66        76        86        96       106       116    |    -   |   136       146       156       166       176       186       196       206       216       226       236       246       256       266       276 
                                                                                                                                  121      130
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: EcoRI] (4)
(-)
Family: EcoRI (4)
(-)
Escherichia coli (4)
1aEcoRI-1qc9C01C:17-273
1bEcoRI-1qc9C02C:17-273
1cEcoRI-1qc9C03C:17-273

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (T2E1_ECOLX | P00642)
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.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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.

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 Related Entries

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        T2E1_ECOLX | P00642: 1ckq 1cl8 1eri 1qps 1qrh 1qri 2oxv

(-) Related Entries Specified in the PDB File

1ckq 1.85 A CRYSTALLOGRAPHIC STRUCTURE OF COGNATE ECORI-DNA COMPLEX