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(-) Description

Title :  CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BFII C-TERMINAL RECOGNITION DOMAIN IN COMPLEX WITH COGNATE DNA
 
Authors :  D. Golovenko, E. Manakova, L. Zakrys, M. Zaremba, G. Sasnauskas, S. Gra V. Siksnys
Date :  03 Jan 13  (Deposition) - 15 Jan 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Hydrolase-Dna Complex, Dna-Binding Pseudobarrel Fold, Dna Recognition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Golovenko, S. Grazulis, E. Manakova, G. Sasnauskas, V. Siksnys, L. Zakrys, M. Zaremba
Structural Insight Into The Specificity Of The B3 Dna-Binding Domains Provided By The Co-Crystal Structure Of The C-Terminal Fragment Of Bfii Restriction Enzyme
Nucleic Acids Res. V. 42 4113 2014
PubMed-ID: 24423868  |  Reference-DOI: 10.1093/NAR/GKT1368
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RESTRICTION ENDONUCLEASE
    Chains: A, D
    EC Number: 3.1.21.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B-BFIIK107A
    Expression System Strain: ER2566
    Expression System Taxid: 562
    Expression System Vector: PET21B
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN BFII-C, RESIDUES 193-358
    Organism Scientific: BACILLUS FIRMUS
    Organism Taxid: 1399
    Other Details: PROTEOLYTIC FRAGMENT OF R.BFIIK107A SPANNING RESIDUES 193-358
    Strain: S8120
    Synonym: R.BFII
 
Molecule 2 - 5'-D(*AP*GP*CP*AP*CP*TP*GP*GP*GP*TP*CP*GP)-3'
    Chains: B, E
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synonym: UPPER DNA STRAND
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*GP*AP*CP*CP*CP*AP*GP*TP*GP*CP*TP)-3'
    Chains: C, F
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synonym: BOTTOM DNA STRAND
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3ZI5)

(-) Sites  (0, 0)

(no "Site" information available for 3ZI5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZI5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZI5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZI5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZI5)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZI5)

(-) 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:166
 aligned with Q9F4C9_BACFI | Q9F4C9 from UniProtKB/TrEMBL  Length:358

    Alignment length:166
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352      
         Q9F4C9_BACFI   193 LDETERVTLIVTLGHADTARIQAAPGTTAGQGTQYFWLSKDSYDFFPPLTIRNRRGTKATYSSLINMNYIDINYTDTQCRVTFEAENNFDFRLGTGKLRYTGVAKSNDIAAITRVGDSDYELRIIKQGTPEHSQLDPYAVSFIGNRGKRFGYISNEEFGRIIGVTF 358
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeeeee.hhhhhhhhhh...hhhhh...eeeehhhhhhhh....ee........eeeeeeeee....eeeeeeeeee.......eeee.hhhh.........eeeeee....eeeeeee...hhhhhhhhhhh.eee....eeeeeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zi5 A 193 LDETERVTLIVTLGHADTARIQAAPGTTAGQGTQYFWLSKDSYDFFPPLTIRNRRGTKATYSSLINMNYIDINYTDTQCRVTFEAENNFDFRLGTGKLRYTGVAKSNDIAAITRVGDSDYELRIIKQGTPEHSQLDPYAVSFIGNRGKRFGYISNEEFGRIIGVTF 358
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352      


Chain B from PDB  Type:DNA  Length:12
                                            
                 3zi5 B   1 AGCACTGGGTCG  12
                                    10  


Chain C from PDB  Type:DNA  Length:12
                                            
                 3zi5 C   1 CGACCCAGTGCT  12
                                    10  


Chain D from PDB  Type:PROTEIN  Length:166
 aligned with Q9F4C9_BACFI | Q9F4C9 from UniProtKB/TrEMBL  Length:358

    Alignment length:166
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352      
         Q9F4C9_BACFI   193 LDETERVTLIVTLGHADTARIQAAPGTTAGQGTQYFWLSKDSYDFFPPLTIRNRRGTKATYSSLINMNYIDINYTDTQCRVTFEAENNFDFRLGTGKLRYTGVAKSNDIAAITRVGDSDYELRIIKQGTPEHSQLDPYAVSFIGNRGKRFGYISNEEFGRIIGVTF 358
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeeeee.hhhhhhhhhh...hhhhh...eee.hhhhhhhh....ee........eeeeeeeee....eeeeeeeeee.......eeee.hhhh.........eeeeee....eeeeeee...hhhhhhhhhhh.eee....eeeeeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zi5 D 193 LDETERVTLIVTLGHADTARIQAAPGTTAGQGTQYFWLSKDSYDFFPPLTIRNRRGTKATYSSLINMNYIDINYTDTQCRVTFEAENNFDFRLGTGKLRYTGVAKSNDIAAITRVGDSDYELRIIKQGTPEHSQLDPYAVSFIGNRGKRFGYISNEEFGRIIGVTF 358
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352      


Chain E from PDB  Type:DNA  Length:12
                                            
                 3zi5 E   1 AGCACTGGGTCG  12
                                    10  


Chain F from PDB  Type:DNA  Length:12
                                            
                 3zi5 F   1 CGACCCAGTGCT  12
                                    10
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3ZI5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZI5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZI5)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (Q9F4C9_BACFI | Q9F4C9)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
biological process
    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

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        Q9F4C9_BACFI | Q9F4C9: 2c1l

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