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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A POST-REACTIVE COGNATE DNA-ECO RI COMPLEX AT 2.50 A IN THE PRESENCE OF MN2+ ION
 
Authors :  M. Horvath, J. Choi, Y. Kim, P. Wilkosz, J. M. Rosenberg
Date :  28 May 99  (Deposition) - 14 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,M,N
Biol. Unit 1:  A,M,N  (2x)
Keywords :  Enzyme, Restriction Endonculease, Protein, Dna, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Horvath, J. Choi, Y. Kim, P. Wilkosz, J. M. Rosenberg
The Integration Of Recognition And Cleavage: X-Ray Structures Of Pre- Transition State And Post-Reactive Dna-Eco Ri Endonuclease Complexes
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*TP*CP*GP*CP*GP*)-3'
    Chains: M
    Engineered: YES
    Other Details: RECOGNITION SEQUENCE
    Synthetic: YES
 
Molecule 2 - 5'-D(*AP*AP*TP*TP*CP*GP*CP*GP*)-3'
    Chains: N
    Engineered: YES
    Other Details: RECOGNITION SEQUENCE
    Synthetic: YES
 
Molecule 3 - ENDONUCLEASE ECORI
    Chains: A
    Fragment: RESIDUES 17-277
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: TYPE II RESTRICTION ENZYME ECORI, R.ECORI

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : AMN
Biological Unit 1 (2x): AMN

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MN1Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:91 , GLU A:111 , ALA A:112 , DA N:6 , HOH N:20 , HOH N:21BINDING SITE FOR RESIDUE MN A 278

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QPS)

(-) 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 d1qpsa_ A: Restriction endonuclease EcoRI                                                                                                                                                                                                                             SCOP domains
               CATH domains 1qpsA00 A:17-277 Eco RI Endonuclease, subunit A                                                                                                                                                                                                                       CATH domains
               Pfam domains EcoRI-1qpsA01 A:17-273                                                                                                                                                                                                                                           ---- Pfam domains
     Sec.struct. author (1) ..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eeee..eehhhhhhhhhh..............ee.....eeeee.....eeeeeeeeeee..hhhhhhhh................hhhhhhhhhhhhhhhhh.......eeeeeehhhhh...eeeee...hhhhh............................................eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeee-------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qps A  17 SQGVIGIFGDYAKAHDLAVGEVSKLVKKALSNEYPQLSFRYRDSIKKTEINEALKKIDPDLGGTLFVSNSSIKPDGGIVEVKDDYGEWRVVLVAEAKHQGKDIINIRNGLLVGKRGDQDLMAAGNAIERSHKNISEIANFMLSESHFPYVLFLEGSNFLTENISITRPDGRVVNLEYNSGILNRLDRLTAANYGMPINSNLCINKFVNHKDKSIMLQAASIYTQGDGREWDSKIMFEIMFDISTTSLRVLGRDLFEQLTSK 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:5
                                     
                 1qps M   1 TCGCG   5


Chain N from PDB  Type:DNA  Length:8
                                        
                 1qps N   6 AATTCGCG  13
   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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1ckq PRE-TRANSITION STATE ECO RI-DNA COGNATE COMPLEX SOLVED TO 1.85 A
1cl8 COGNATE ECORI-DNA STRUCTURE WITH THE INNER ADENINE OF RECOGNITION SEQUENCE GAATTC REPLACED WITH BASE ANALOG PURINE
1qc9 STRUCTURE OF ECORI SOLVED IN ABSENCE OF DNA