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(-) Description

Title :  X-RAY STRUCTURE OF THE DNA-ECO RI ENDONUCLEASE COMPLEXES WITH AN E144D MUTATION AT 2.7 A
 
Authors :  J. Choi, Y. Kim, P. Greene, P. Hager, J. M. Rosenberg
Date :  14 Jun 99  (Deposition) - 23 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,M
Biol. Unit 1:  A,M  (2x)
Keywords :  Restriction Endonuclease, Dna-Protein Complex, Site- Directed Mutation, Sequence-Specific, X-Ray Crystallography, Protein Structure, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Choi, Y. Kim, P. Greene, P. Hager, J. M. Rosenberg
X-Ray Structure Of The Dna-Eco Ri Endonuclease Complexes With The Ed144 And Rk145 Mutations
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*TP*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
    Chains: M
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - ECO RI ENDONCULEASE
    Chains: A
    Fragment: RESIDUES 17-277
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AM
Biological Unit 1 (2x): AM

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QRI)

(-) 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:261
 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 d1qria_ A: Restriction endonuclease EcoRI                                                                                                                                                                                                                             SCOP domains
               CATH domains 1qriA00 A:17-277 Eco RI Endonuclease, subunit A                                                                                                                                                                                                                       CATH domains
               Pfam domains EcoRI-1qriA01 A:17-273                                                                                                                                                                                                                                           ---- Pfam domains
     Sec.struct. author (1) ..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...eeeee..eehhhhhhhhhh..............ee.....eeeee.....eeeeeeeeeee..hhhhhhhh................hhhhhhhhhhhhhhhhh.......eeeeee........eeee....hhhhh.............................eee......eee...eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeee-------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qri A  17 SQGVIGIFGDYAKAHDLAVGEVSKLVKKALSNEYPQLSFRYRDSIKKTEINEALKKIDPDLGGTLFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDIINIRNGLLVGKRGDQDLMAAGNAIDRSHKNISEIANFMLSESHFPYVLFLEGSNFLTENISITRPDGRVVNLEYNSGILNRLDRLTAANYGMPINSNLCINKFVNHKDKSIMLQAASIYTQGDGREWDSKIMFEIMFDISTTSLRVLGRDLFEQLTSK 277
                                    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 


Chain M from PDB  Type:DNA  Length:13
                                             
                 1qri M   1 TCGCGAATTCGCG  13
                                    10
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: EcoRI] (4)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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  T2E1_ECOLX | P00642
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 Related Entries

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

UniProtKB/Swiss-Prot
        T2E1_ECOLX | P00642: 1ckq 1cl8 1eri 1qc9 1qps 1qrh 2oxv

(-) Related Entries Specified in the PDB File

1ckq 1.85 A COGNATE PRE-TRANSITION STATE ECORI-DNA CRYSTAL STRUCTURE
1cl8 1.80 A CRYSTAL STRUCTURE OF A COGNATE ECO RI-DNA COMPLEX WITH A BASE ANALOG SUBSTITUTION IN THE DNA RECOGNITION REGION
1qc9 3.3 A CRYSTAL STRUCTURE OF ECO RI DIMER IN THE ABSENCE OF DNA
1qps 2.5 A COGNATE POST-REACTIVE ECO-RI DNA CRYSTAL STRUCTURE IN THE PRESENCE OF MN2+