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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH MG+2 AND DSDNA (RESOLUTION 2.9A)
 
Authors :  M. J. Mate, C. Kleanthous
Date :  06 Apr 04  (Deposition) - 23 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
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, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MG6Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:102 , HIS A:127 , DT E:5 , DC E:6BINDING SITE FOR RESIDUE MG A1134
2AC2SOFTWAREHIS C:102 , HIS C:127 , DT I:5 , DC I:6BINDING SITE FOR RESIDUE MG C1134
3AC3SOFTWAREDG E:3 , DG L:9 , DC L:10BINDING SITE FOR RESIDUE MG E1009
4AC4SOFTWAREDG G:3 , DC J:10BINDING SITE FOR RESIDUE MG G1009
5AC5SOFTWAREDC H:10 , DG I:3BINDING SITE FOR RESIDUE MG I1009
6AC6SOFTWAREDC F:10 , DG K:3BINDING SITE FOR RESIDUE MG K1009

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V14)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V14)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V14)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V14)

(-) Exons   (0, 0)

(no "Exon" information available for 1V14)

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

    Alignment length:132
                                   459       469       479       489       499       509       519       529       539       549       559       569       579  
           CEA9_ECOLX   450 ESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRG 581
               SCOP domains d1v14a_ A: DNase domain of colicin E9                                                                                                SCOP domains
               CATH domains 1v14A00 A:2-133 Colicin e7 immunity protein. Chain B                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......ee........................hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhh......hhhhh.......eeee..hhhhh........eeeehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v14 A   2 ESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHADKPISQGGEVYDMDNIRVTTPKRHIDIHRG 133
                                    11        21        31        41        51        61        71        81        91       101       111       121       131  


Chain B from PDB  Type:PROTEIN  Length:132
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:132
                                   458       468       478       488       498       508       518       528       538       548       558       568       578  
           CEA9_ECOLX   449 KESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHR 580
               SCOP domains d1v14b_ B: DNase domain of colicin E9                                                                                                SCOP domains
               CATH domains 1v14B00 B:1-132 Colicin e7 immunity protein. Chain B                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........ee.........hhhhhhhh....ee.hhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhh.......eeee..hhhhh........eeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v14 B   1 MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHADKPISQGGEVYDMDNIRVTTPKRHIDIHR 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  


Chain C from PDB  Type:PROTEIN  Length:132
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:132
                                   459       469       479       489       499       509       519       529       539       549       559       569       579  
           CEA9_ECOLX   450 ESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRG 581
               SCOP domains d1v14c_ C: DNase domain of colicin E9                                                                                                SCOP domains
               CATH domains 1v14C00 C:2-133 Colicin e7 immunity protein. Chain B                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......ee..........hhhhhhhh......hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee...............eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v14 C   2 ESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHADKPISQGGEVYDMDNIRVTTPKRHIDIHRG 133
                                    11        21        31        41        51        61        71        81        91       101       111       121       131  


Chain D from PDB  Type:PROTEIN  Length:130
 aligned with CEA9_ECOLX | P09883 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:130
                                   461       471       481       491       501       511       521       531       541       551       561       571       581
           CEA9_ECOLX   452 KRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRG 581
               SCOP domains d1v14d_ D: DNase domain of colicin E9                                                                                              SCOP domains
               CATH domains 1v14D00 D:4-133 Colicin e7 immunity protein. Chain B                                                                               CATH domains
           Pfam domains (1) Colicin-DNase-1v14D01 D:4-133                                                                                                      Pfam domains (1)
           Pfam domains (2) Colicin-DNase-1v14D02 D:4-133                                                                                                      Pfam domains (2)
           Pfam domains (3) Colicin-DNase-1v14D03 D:4-133                                                                                                      Pfam domains (3)
           Pfam domains (4) Colicin-DNase-1v14D04 D:4-133                                                                                                      Pfam domains (4)
         Sec.struct. author .....ee..........hhhhhhhh......hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee..hhhhh........eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v14 D   4 KRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHADKPISQGGEVYDMDNIRVTTPKRHIDIHRG 133
                                    13        23        33        43        53        63        73        83        93       103       113       123       133


Chain E from PDB  Type:DNA  Length:6
                                      
                 1v14 E   3 GATCGC   8


Chain F from PDB  Type:DNA  Length:8
                                        
                 1v14 F   9 GCGATCGC  16


Chain G from PDB  Type:DNA  Length:6
                                      
                 1v14 G   3 GATCGC   8


Chain H from PDB  Type:DNA  Length:8
                                        
                 1v14 H   9 GCGATCGC  16


Chain I from PDB  Type:DNA  Length:6
                                      
                 1v14 I   3 GATCGC   8


Chain J from PDB  Type:DNA  Length:8
                                        
                 1v14 J   9 GCGATCGC  16


Chain K from PDB  Type:DNA  Length:6
                                      
                 1v14 K   3 GATCGC   8


Chain L from PDB  Type:DNA  Length:8
                                        
                 1v14 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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  1v14
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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 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
1v13 CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE DOMAIN IN COMPLEX WITH ZN+2 (2.0 ANGSTROMS)
1v15 CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE DOMAIN IN COMPLEX WITH ZN+2 (2.0 ANGSTROMS)