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(-) Description

Title :  STRUCTURE OF RESTRICTION ENDONUCLEASE BSTYI BOUND TO NON-COGNATE DNA
 
Authors :  S. A. Townson, J. C. Samuelson, Y. Bao, S. Y. Xu, A. K. Aggarwal
Date :  28 Feb 07  (Deposition) - 01 May 07  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Restriction Endonuclease, Dna Recognition, Scanning, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Townson, J. C. Samuelson, Y. Bao, S. Y. Xu, A. K. Aggarwal
Bstyi Bound To Noncognate Dna Reveals A "Hemispecific" Complex: Implications For Dna Scanning.
Structure V. 15 449 2007
PubMed-ID: 17437717  |  Reference-DOI: 10.1016/J.STR.2007.03.002

(-) Compounds

Molecule 1 - 5'-D(*AP*TP*GP*AP*AP*TP*CP*CP*AP*TP*A)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*TP*AP*TP*GP*GP*AP*TP*TP*CP*AP*T)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - BSTYI
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYC, PCEF8, PET21AT
    Expression System Strain: ER2744
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BSTYIR
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2P0J)

(-) Sites  (0, 0)

(no "Site" information available for 2P0J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P0J)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:191 -Pro A:192
2Val B:191 -Pro B:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P0J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P0J)

(-) Exons   (0, 0)

(no "Exon" information available for 2P0J)

(-) Sequences/Alignments

Asymmetric/Biological 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:203
 aligned with Q84AF2_GEOSE | Q84AF2 from UniProtKB/TrEMBL  Length:203

    Alignment length:203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   
         Q84AF2_GEOSE     1 MRIVEVYSHLNGLEYIQVHLPHIWEEIQEIIVSIDAEACRTKESKEKTKQGQILYSPVALNEAFKEKLEAKGWKESRTNYYVTADPKLIRETLSLEPEEQKKVIEAAGKEALKSYNQTDFVKDRVAIEVQFGKYSFVAYDLFVKHMAFYVSDKIDVGVEILPMKELSKEMSSGISYYEGELYNVIRQGRGVPAVPLVLIGIAP 203
               SCOP domains d2p0ja_ A: Restriction endonuclease BstyI                                                                                                                                                                   SCOP domains
               CATH domains 2p0jA00 A:1-203  [code=3.40.91.20, no name defined]                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee..hhhhh..ee.hhhhhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhh..hhhhhhhhhhhh....eeeeeeeeeee..eeeee...hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhh.......hhhhhhhhhhh.........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p0j A   1 MRIVEVYSHLNGLEYIQVHLPHIWEEIQEIIVSIDAEACRTKESKEKTKQGQILYSPVALNEAFKEKLEAKGWKESRTNYYVTADPKLIRETLSLEPEEQKKVIEAAGKEALKSYNQTDFVKDRVAIEVQFGKYSFVAYDLFVKHMAFYVSDKIDVGVEILPMKELSKEMSSGISYYEGELYNVIRQGRGVPAVPLVLIGIAP 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   


Chain B from PDB  Type:PROTEIN  Length:196
 aligned with Q84AF2_GEOSE | Q84AF2 from UniProtKB/TrEMBL  Length:203

    Alignment length:203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   
         Q84AF2_GEOSE     1 MRIVEVYSHLNGLEYIQVHLPHIWEEIQEIIVSIDAEACRTKESKEKTKQGQILYSPVALNEAFKEKLEAKGWKESRTNYYVTADPKLIRETLSLEPEEQKKVIEAAGKEALKSYNQTDFVKDRVAIEVQFGKYSFVAYDLFVKHMAFYVSDKIDVGVEILPMKELSKEMSSGISYYEGELYNVIRQGRGVPAVPLVLIGIAP 203
               SCOP domains d2p0jb_ B: Restriction endonuclease BstyI                                                                                                                                                                   SCOP domains
               CATH domains 2p0jB00 B:1-203  [code=3.40.91.20, no name def       ined]                                                                                                                                                  CATH domains
           Pfam domains (1) ----------Endonuc-BglII-2p0jB01 B:11-202                                                                                                                                                                  - Pfam domains (1)
           Pfam domains (2) ----------Endonuc-BglII-2p0jB02 B:11-202                                                                                                                                                                  - Pfam domains (2)
         Sec.struct. author .eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......-------..hhhhhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhh..hhhhhhhhhhhh....eeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhh....eeeeeeehhhhhh.......hhhhhhhhhhh.........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p0j B   1 MRIVEVYSHLNGLEYIQVHLPHIWEEIQEIIVSIDAEACRTKESKE-------LYSPVALNEAFKEKLEAKGWKESRTNYYVTADPKLIRETLSLEPEEQKKVIEAAGKEALKSYNQTDFVKDRVAIEVQFGKYSFVAYDLFVKHMAFYVSDKIDVGVEILPMKELSKEMSSGISYYEGELYNVIRQGRGVPAVPLVLIGIAP 203
                                    10        20        30        40     |   -   |    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   
                                                                        46      54                                                                                                                                                     


Chain C from PDB  Type:DNA  Length:11
                                           
                 2p0j C   1 ATGAATCCATA  11
                                    10 


Chain D from PDB  Type:DNA  Length:11
                                           
                 2p0j D   1 TATGGATTCAT  11
                                    10
   Legend:   → Mismatch (orange background)
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  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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PDDEXK (13)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q84AF2_GEOSE | Q84AF2)
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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
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.

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  Cis Peptide Bonds
    Val A:191 - Pro A:192   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        Q84AF2_GEOSE | Q84AF2: 1sdo 1vrr

(-) Related Entries Specified in the PDB File

1sd0 CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BSTYI
1vrr CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BSTYI COMPLEX WITH DNA