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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE DOMAIN IN COMPLEX WITH ZN+2 (2.0 ANGSTROMS)
 
Authors :  M. J. Mate, C. Kleanthous
Date :  06 Apr 04  (Deposition) - 23 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Homing Endonucleases, Colicins, Beta-Beta-Alpha Metal Antibiotic, Bacteriocin, Hydrolase, Endonuclease Motif, H-N-H Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Mate, C. Kleanthous
Structure-Based Analysis Of The Metal-Dependent Mechanism Of H-N-H Endonucleases
J. Biol. Chem. V. 279 34763 2004
PubMed-ID: 15190054  |  Reference-DOI: 10.1074/JBC.M403719200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLICIN E9
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC 99A (PRJ352)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:102 , HIS A:127 , HIS A:131 , HOH A:2027BINDING SITE FOR RESIDUE ZN A 200
2AC2SOFTWAREHIS B:102 , HIS B:127 , HIS B:131 , HOH B:2064 , HOH B:2065BINDING SITE FOR RESIDUE ZN B 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V13)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V13)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V13)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V13)

(-) Exons   (0, 0)

(no "Exon" information available for 1V13)

(-) 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:120
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:126
                                   465       475       485       495       505       515       525       535       545       555       565       575      
           CEA9_ECOLX   456 PGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRG 581
               SCOP domains d1v13a_ A:    DNase domain of colicin E9                                                                                       SCOP domains
               CATH domains 1v13A00 A:   8-133 Colicin e7 immunity protein. Chain B                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....---hhhhh......ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhh..--..-.hhhhhhhhhh......hhhhh.......eeee.........eee...eeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v13 A   8 PGKATGKGKP---KWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDP--SK-LNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHADKPISQGGEVYDMDNIRVTTPKRHIDIHRG 133
                                    17   |    27        37        47        57       | -|| |    77        87        97       107       117       127      
                                    17  21                                          65 68| |                                                              
                                                                                        69 |                                                              
                                                                                          71                                                              


Chain B from PDB  Type:PROTEIN  Length:126
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:126
                                   465       475       485       495       505       515       525       535       545       555       565       575      
           CEA9_ECOLX   456 PGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRG 581
               SCOP domains d1v13b_ B: DNase domain of colicin E9                                                                                          SCOP domains
               CATH domains 1v13B00 B:8-133 Colicin e7 immunity protein. Chain B                                                                           CATH domains
           Pfam domains (1) Colicin-DNase-1v13B01 B:8-133                                                                                                  Pfam domains (1)
           Pfam domains (2) Colicin-DNase-1v13B02 B:8-133                                                                                                  Pfam domains (2)
         Sec.struct. author .eeee........hhhhhhhh...ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee.........eee...eeeehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v13 B   8 PGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHADKPISQGGEVYDMDNIRVTTPKRHIDIHRG 133
                                    17        27        37        47        57        67        77        87        97       107       117       127
   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) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: His-Me_finger (38)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CEA9_ECOLX | P09883)
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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  1v13
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  CEA9_ECOLX | P09883
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  3.1.-.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        CEA9_ECOLX | P09883: 1bxi 1emv 1fr2 1fsj 1v14 1v15 2gyk 2gze 2gzf 2gzg 2gzi 2gzj 2ivz 2k5x 2vln 2vlo 2vlp 2vlq 2wpt 3o0e 4jml 5ew5

(-) Related Entries Specified in the PDB File

1bxi CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI COLICIN E9 DNASEDOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9
1emv CRYSTAL STRUCTURE OF COLICIN E9 DNASE DOMAIN WITH ITSCOGNATE IMMUNITY PROTEIN IM9 (1.7 ANGSTROMS)
1fr2 CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN WITH A MUTANTIMMUNITY PROTEIN IM9(E41A)
1fsj CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN
1v14 CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH MG+2 AND DSDNA (RESOLUTION 2.9A)
1v15 COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH ZN+2 AND DOUBLE STRAND DNA