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(-) Description

Title :  RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX)
 
Authors :  H. Viadiu, A. K. Aggarwal
Date :  19 Aug 98  (Deposition) - 13 Jan 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Hydrolase, Phosphodiesterase, Complex (Endonuclease/Dna), Nuclease, Protein/Dna, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Viadiu, A. K. Aggarwal
The Role Of Metals In Catalysis By The Restriction Endonuclease Bamhi.
Nat. Struct. Biol. V. 5 910 1998
PubMed-ID: 9783752  |  Reference-DOI: 10.1038/2352
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)- 3')
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(*TP*AP*TP*G)-3')
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*GP*AP*TP*CP*CP*AP*TP*A)-3')
    Chains: E
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - PROTEIN (RESTRICTION ENDONUCLEASE BAMHI)
    Chains: A, B
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS AMYLOLIQUEFACIENS
    Organism Taxid: 1390
    Other Details: CRYSTAL GROWN IN THE PRESENCE OF MANGANESE IONS.
    Synonym: R. BAMHI

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:94 , PHE A:112 , HOH A:902 , DG E:1BINDING SITE FOR RESIDUE MN A 901
2AC2SOFTWAREPRO A:92 , ASP A:94 , GLU A:111 , HOH A:903 , DG D:4BINDING SITE FOR RESIDUE MN D 902
3CTAAUTHORGLU A:77 , ASP A:94 , GLU A:111 , GLU A:113CATALYTIC SITE R-SUBUNIT.
4CTBAUTHORGLU B:77 , ASP B:94 , GLU B:111 , GLU B:113CATALYTIC SITE L-SUBUNIT.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BAM)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:38 -Pro A:39
2Trp B:38 -Pro B:39

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BAM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BAM)

(-) Exons   (0, 0)

(no "Exon" information available for 3BAM)

(-) 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:206
 aligned with T2BA_BACAM | P23940 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
           T2BA_BACAM     1 MEVEKEFITDEAKELLSKDKLIQQAYNEVKTSICSPIWPATSKTFTINNTEKNCNGVVPIKELCYTLLEDTYNWYREKPLDILKLEKKKGGPIDVYKEFIENSELKRVGMEFETGNISSAHRSMNKLLLGLKHGEIDLAIILMPIKQLAYYLTDRVTNFEELEPYFELTEGQPFIFIGFNAEAYNSNVPLIPKGSDGMSKRSIKKW 206
               SCOP domains d3bama_ A: Restriction endonuclease BamHI                                                                                                                                                                      SCOP domains
               CATH domains 3bamA00 A:1-206  [code=3.40.91.20, no name defined]                                                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhh.hhhhhhhhhhhhhhhh..........eee.........hhhhhhhhhhhhh..........hhhh..........eeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhhh.....eeeeeee.hhhhhh.......hhhhhhhhhhh....eeeeeee..eee..................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bam A   1 MEVEKEFITDEAKELLSKDKLIQQAYNEVKTSICSPIWPATSKTFTINNTEKNCNGVVPIKELCYTLLEDTYNWYREKPLDILKLEKKKGGPIDVYKEFIENSELKRVGMEFETGNISSAHRSMNKLLLGLKHGEIDLAIILMPIKQLAYYLTDRVTNFEELEPYFELTEGQPFIFIGFNAEAYNSNVPLIPKGSDGMSKRSIKKW 206
                                    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:209
 aligned with T2BA_BACAM | P23940 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
           T2BA_BACAM     1 MEVEKEFITDEAKELLSKDKLIQQAYNEVKTSICSPIWPATSKTFTINNTEKNCNGVVPIKELCYTLLEDTYNWYREKPLDILKLEKKKGGPIDVYKEFIENSELKRVGMEFETGNISSAHRSMNKLLLGLKHGEIDLAIILMPIKQLAYYLTDRVTNFEELEPYFELTEGQPFIFIGFNAEAYNSNVPLIPKGSDGMSKRSIKKWKDK 209
               SCOP domains d3bamb_ B: Restriction endonuclease BamHI                                                                                                                                                                         SCOP domains
               CATH domains 3bamB00 B:1-209  [code=3.40.91.20, no name defined]                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhh.hhhhhhhhhhhhhhhh......................hhhhhhhhhhhhh..........hhhh..........eeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhhh.....eeeeeee.hhhhhh.......hhhhhhhhhhh....eeeeeee.............hhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bam B   1 MEVEKEFITDEAKELLSKDKLIQQAYNEVKTSICSPIWPATSKTFTINNTEKNCNGVVPIKELCYTLLEDTYNWYREKPLDILKLEKKKGGPIDVYKEFIENSELKRVGMEFETGNISSAHRSMNKLLLGLKHGEIDLAIILMPIKQLAYYLTDRVTNFEELEPYFELTEGQPFIFIGFNAEAYNSNVPLIPKGSDGMSKRSIKKWKDK 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         


Chain C from PDB  Type:DNA  Length:12
                                            
                 3bam C   1 TATGGATCCATA  12
                                    10  


Chain D from PDB  Type:DNA  Length:4
                                    
                 3bam D   1 TATG   4


Chain E from PDB  Type:DNA  Length:7
                                       
                 3bam E   1 GATCCAT   7
   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, 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  (0, 0)

(no "Pfam Domain" information available for 3BAM)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (T2BA_BACAM | P23940)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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.
    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.
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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  3bam
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  3.1.21.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        T2BA_BACAM | P23940: 1bam 1bhm 1esg 2bam

(-) Related Entries Specified in the PDB File

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