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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NUCLEASE DOMAIN OF COLE7(D493Q MUTANT) IN COMPLEX WITH AN 18-BP DUPLEX DNA
 
Authors :  Y. T. Wang, L. G. Doudeva, H. S. Yuan
Date :  19 Nov 08  (Deposition) - 03 Nov 09  (Release) - 03 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Computational Redesign, Protein Engineering, Protein-Nucleic Acid Interactions, Dnase, Dna Hydrolysis. , Antibiotic, Antimicrobial, Bacteriocin, Endonuclease, Hydrolase, Metal- Binding, Nuclease, Plasmid, Zinc, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. T. Wang, J. D. Wright, L. G. Doudeva, H. C. Jhang, C. Lim, H. S. Yuan
Redesign Of High-Affinity Nonspecific Nucleases With Altered Sequence Preference
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLICIN-E7
    Chains: A, D
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE70
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NUCLEASE DOMAIN
    Gene: CEA, COLE7
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: W3110
 
Molecule 2 - 5'- D(*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DGP*DAP*DTP*DCP*DGP*DAP*DAP* DTP*DTP*DCP*DC)-3'
    Chains: B, C, E, F
    Engineered: YES
    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 3FBD)

(-) Sites  (0, 0)

(no "Site" information available for 3FBD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FBD)

(-) 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:132
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:132
                                   454       464       474       484       494       504       514       524       534       544       554       564       574  
           CEA7_ECOLX   445 SKRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
               SCOP domains d3fbda_ A: automated matches                                                                                                         SCOP domains
               CATH domains 3fbdA00 A:445-576 Colicin e7 immunity protein. Chain B                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......ee...........hhhhh.....ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhh.......eeee..hhhhh........eeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fbd A 445 SKRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFQDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
                                   454       464       474       484       494       504       514       524       534       544       554       564       574  


Chain B from PDB  Type:DNA  Length:18
                                                  
                 3fbd B   1 GGAATTCGATCGAATTCC  18
                                    10        


Chain C from PDB  Type:DNA  Length:18
                                                  
                 3fbd C  19 GGAATTCGATCGAATTCC  36
                                    28        


Chain D from PDB  Type:PROTEIN  Length:131
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:131
                                   455       465       475       485       495       505       515       525       535       545       555       565       575 
           CEA7_ECOLX   446 KRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
               SCOP domains d3fbdd_ D: automated matches                                                                                                        SCOP domains
               CATH domains 3fbdD00 D:446-576 Colicin e7 immunity protein. Chain B                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..........hhhhhhh....ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhh.......eeee...............eeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fbd D 446 KRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFQDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK 576
                                   455       465       475       485       495       505       515       525       535       545       555       565       575 


Chain E from PDB  Type:DNA  Length:18
                                                  
                 3fbd E   1 GGAATTCGATCGAATTCC  18
                                    10        


Chain F from PDB  Type:DNA  Length:18
                                                  
                 3fbd F  19 GGAATTCGATCGAATTCC  36
                                    28
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (CEA7_ECOLX | Q47112)
molecular function
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005727    extrachromosomal circular DNA    Circular DNA structures that are not part of a chromosome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CEA7_ECOLX | Q47112: 1m08 1mz8 1pt3 1ujz 1zns 1znv 2axc 2erh 2ivh 2jaz 2jb0 2jbg 3gjn 3gkl 3zfk 7cei

(-) Related Entries Specified in the PDB File

1pt3 CRYSTAL STRUCTURES OF NUCLEASE-COLE7 COMPLEXED WITH OCTAMER DNA
1zns CRYSTAL STRUCTURE OF N-COLE7/12-BP DNA/ZN COMPLEX
2ivh CRYSTAL STRUCTURES OF NUCLEASE-COLE7 COMPLEXED WITH OCTAMER DNA