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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RESTRICTION ENDONUCLEASE BGLI (E.C.3.1.21.4) BOUND TO ITS DNA RECOGNITION SEQUENCE
 
Authors :  M. Newman, K. Lunnen, G. Wilson, J. Greci, I. Schildkraut, S. E. V. Phillips
Date :  15 Dec 99  (Deposition) - 18 Dec 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,F
Biol. Unit 1:  A,F  (2x)
Keywords :  Protein-Dna Complex, Active Site Calcium Ions, Alpha/Beta Structure, A:A Mismatch, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Newman, K. Lunnen, G. Wilson, J. Greci, I. Schildkraut, S. E. Phillips
Crystal Structure Of Restriction Endonuclease Bgli Bound To Its Interrupted Dna Recognition Sequence.
Embo J. V. 17 5466 1998
PubMed-ID: 9736624  |  Reference-DOI: 10.1093/EMBOJ/17.18.5466
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*AP*TP*CP*GP*CP*CP*TP*AP*AP*TP*AP*GP*GP*CP*GP*AP*T)-3')
    Chains: F
    Engineered: YES
    Other Details: CONTAINS DNA RECOGNITION SEQUENCE OF BGLI
    Synthetic: YES
 
Molecule 2 - BGLI RESTRICTION ENDONUCLEASE
    Chains: A
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CA4Ligand/IonCALCIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:116 , ASP A:142 , ILE A:143 , HOH A:304 , DA F:2 , HOH F:10BINDING SITE FOR RESIDUE CA A 300
2AC2SOFTWAREASP A:116 , HOH A:305 , HOH A:306 , HOH A:307 , DT F:1 , DA F:2 , HOH F:11BINDING SITE FOR RESIDUE CA F 9
3AC3SOFTWAREGLY A:77 , HOH A:374 , HOH A:382 , HOH A:383 , HOH A:384 , HOH A:385 , HOH A:386BINDING SITE FOR RESIDUE CA A 301
4AC4SOFTWARESER A:99 , ARG A:101 , GLU A:102 , ILE A:104 , HOH A:397 , HOH A:425 , HOH A:426BINDING SITE FOR RESIDUE CA A 302
5AC5SOFTWAREGLU A:21 , ASN A:165 , ASP A:167 , PHE A:247 , CYS A:248BINDING SITE FOR RESIDUE BME A 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:249 -Pro A:250

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DMU)

(-) 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:299
 aligned with T2B1_BACIU | O68557 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         
           T2B1_BACIU     1 MYNLHREKIFMSYNQNKQYLEDNPEIQEKIELYGLNLLNEVISDNEEEIRADYNEANFLHPFWMNYPPLDRGKMPKGDQIPWIEVGEKAVGSKLTRLVSQREDITVREIGLPTGPDERYLLTSPTIYSLTNGFTDSIMMFVDIKSVGPRDSDYDLVLSPNQVSGNGDWAQLEGGIQNNQQTIQGPRSSQIFLPTIPPLYILSDGTIAPVVHLFIKPIYAMRSLTKGDTGQSLYKIKLASVPNGLGLFCNPGYAFDSAYKFLFRPGKDDRTKSLLQKRVRVDLRVLDKIGPRVMTIDMDK 299
               SCOP domains d1dmua_ A: Restriction endonuclease BglI                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1dmuA00 A:1-299  [code=3.40.600.20, no name defined]                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh....eee.........eeeeeehhhhhhhh.....eeeeeeee..........eeeehhhhh.................eeee....eeee......eee.....eeeeeeeeeeeeeee.hhh.....eeeeeeeeeee.hhhhhhh..hhhhhhhhh..eee.............eeeehhhhh.....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dmu A   1 MYNLHREKIFMSYNQNKQYLEDNPEIQEKIELYGLNLLNEVISDNEEEIRADYNEANFLHPFWMNYPPLDRGKMPKGDQIPWIEVGEKAVGSKLTRLVSQREDITVREIGLPTGPDERYLLTSPTIYSLTNGFTDSIMMFVDIKSVGPRDSDYDLVLSPNQVSGNGDWAQLEGGIQNNQQTIQGPRSSQIFLPTIPPLYILSDGTIAPVVHLFIKPIYAMRSLTKGDTGQSLYKIKLASVPNGLGLFCNPGYAFDSAYKFLFRPGKDDRTKSLLQKRVRVDLRVLDKIGPRVMTIDMDK 299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         


Chain F from PDB  Type:DNA  Length:17
                                                 
                 1dmu F  -8 ATCGCCTAATAGGCGAT   8
                                     1
   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  (0, 0)

(no "Pfam Domain" information available for 1DMU)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (T2B1_BACIU | O68557)
molecular function
    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: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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