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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH ZN+2 AND DSDNA (RESOLUTION 2.4A)
 
Authors :  M. J. Mate, C. Kleanthous
Date :  06 Apr 04  (Deposition) - 23 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,E,F  (1x)
Biol. Unit 2:  B,G,H  (1x)
Biol. Unit 3:  C,I,J  (1x)
Biol. Unit 4:  D,K,L  (1x)
Keywords :  Homing Endonucleases, Colicin, Hnh Motif, Beta-Beta-Alpha Metal Motif, Hydrolase (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, C, D
    EC Number: 3.1.21.1
    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
    Fragment: C-TERMINAL DOMAIN, RESIDUES 450-582
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
    Chains: E, F, G, H, I, J, K, L
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): A   EF      
Biological Unit 2 (1x):  B    GH    
Biological Unit 3 (1x):   C     IJ  
Biological Unit 4 (1x):    D      KL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1ZN8Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:102 , HIS A:127 , HIS A:131 , DT E:5 , DC E:6BINDING SITE FOR RESIDUE ZN A1132
2AC2SOFTWAREHIS B:102 , HIS B:127 , HIS B:131 , DT G:5 , DC G:6BINDING SITE FOR RESIDUE ZN B1135
3AC3SOFTWAREHIS C:102 , HIS C:127 , HIS C:131 , DT I:5 , DC I:6BINDING SITE FOR RESIDUE ZN C1132
4AC4SOFTWAREHIS D:102 , HIS D:127 , HIS D:131 , DT K:5 , DC K:6BINDING SITE FOR RESIDUE ZN D1135
5AC5SOFTWAREDG E:3 , HOH E:2004 , DG L:9 , DC L:10BINDING SITE FOR RESIDUE ZN E1009
6AC6SOFTWAREDG G:3 , HOH G:2009 , DC J:10BINDING SITE FOR RESIDUE ZN G1009
7AC7SOFTWAREDC H:10 , DG I:3 , HOH I:2006BINDING SITE FOR RESIDUE ZN I1009
8AC8SOFTWAREDC F:10 , DG K:3BINDING SITE FOR RESIDUE ZN K1009

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V15)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V15)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V15)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V15)

(-) Exons   (0, 0)

(no "Exon" information available for 1V15)

(-) 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:106
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:129
                                   460       470       480       490       500       510       520       530       540       550       560       570         
           CEA9_ECOLX   451 SKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIH 579
               SCOP domains d1v15a_ A: DNase domain of colic             in E9                                                                                SCOP domains
               CATH domains 1v15A00 A:3-131 Colicin e7 immun             ity protein. Chain           B                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................-------------.hhhhhhhhhhhhhhhh.----------hhhhhhh.....hhhhh.......eeee...............eeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v15 A   3 SKRNKPGKATGKGKPVGDKWLDDAGKDSGAPI-------------KSFDDFRKAVWEEVSKDP----------KSSVSKGYSPFTPKNQQVGGRKVYELHADKPISQGGEVYDMDNIRVTTPKRHIDIH 131
                                    12        22        32 |       -     |  52        62  |      -   |    82        92       102       112       122         
                                                          34            48               65         76                                                       


Chain B from PDB  Type:PROTEIN  Length:134
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:134
                                   458       468       478       488       498       508       518       528       538       548       558       568       578    
           CEA9_ECOLX   449 KESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 582
               SCOP domains d1v15b_ B: DNase domain of colicin E9                                                                                                  SCOP domains
               CATH domains 1v15B00 B:1-134 Colicin e7 immunity protein. Chain B                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee........hhhhhhhhhh...ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh......hhhhh.......eeee...............eeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v15 B   1 MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHADKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    


Chain C from PDB  Type:PROTEIN  Length:129
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:129
                                   460       470       480       490       500       510       520       530       540       550       560       570         
           CEA9_ECOLX   451 SKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIH 579
               SCOP domains d1v15c_ C: DNase domain of colicin E9                                                                                             SCOP domains
               CATH domains 1v15C00 C:3-131 Colicin e7 immunity protein. Chain B                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.............hhhhh......hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh......hhhhh.......eeee...............eeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v15 C   3 SKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHADKPISQGGEVYDMDNIRVTTPKRHIDIH 131
                                    12        22        32        42        52        62        72        82        92       102       112       122         


Chain D from PDB  Type:PROTEIN  Length:133
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:133
                                   459       469       479       489       499       509       519       529       539       549       559       569       579   
           CEA9_ECOLX   450 ESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 582
               SCOP domains d1v15d_ D: DNase domain of colicin E9                                                                                                 SCOP domains
               CATH domains 1v15D00 D:2-134 Colicin e7 immunity protein. Chain B                                                                                  CATH domains
           Pfam domains (1) -Colicin-DNase-1v15D01 D:3-133                                                                                                      - Pfam domains (1)
           Pfam domains (2) -Colicin-DNase-1v15D02 D:3-133                                                                                                      - Pfam domains (2)
           Pfam domains (3) -Colicin-DNase-1v15D03 D:3-133                                                                                                      - Pfam domains (3)
           Pfam domains (4) -Colicin-DNase-1v15D04 D:3-133                                                                                                      - Pfam domains (4)
         Sec.struct. author .......ee..........hhhhhhhh......hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee...............eeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v15 D   2 ESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHADKPISQGGEVYDMDNIRVTTPKRHIDIHRGK 134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   


Chain E from PDB  Type:DNA  Length:7
                                       
                 1v15 E   2 CGATCGC   8


Chain F from PDB  Type:DNA  Length:8
                                        
                 1v15 F   9 GCGATCGC  16


Chain G from PDB  Type:DNA  Length:6
                                      
                 1v15 G   3 GATCGC   8


Chain H from PDB  Type:DNA  Length:8
                                        
                 1v15 H   9 GCGATCGC  16


Chain I from PDB  Type:DNA  Length:7
                                       
                 1v15 I   2 CGATCGC   8


Chain J from PDB  Type:DNA  Length:8
                                        
                 1v15 J   9 GCGATCGC  16


Chain K from PDB  Type:DNA  Length:6
                                      
                 1v15 K   3 GATCGC   8


Chain L from PDB  Type:DNA  Length:8
                                        
                 1v15 L   9 GCGATCGC  16
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  1v15
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  CEA9_ECOLX | P09883
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  3.1.21.1
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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 1v13 1v14 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 DNASE DOMAIN 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
1v13 CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE DOMAIN IN COMPLEX WITH ZN+2
1v14 CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE DOMAIN IN COMPLEX WITH MG+2