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(-) Description

Title :  N-TERMINAL TRUNCATED NUCLEASE DOMAIN OF COLICIN E7
 
Authors :  E. Toth, A. Czene, B. Gyurcsik, H. Otten, J. -C. N. Poulsen, S. Larsen, H. E. M. Christensen, K. Nagata
Date :  11 Dec 12  (Deposition) - 18 Dec 13  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Artificial Metallonuclease, Allosteric Control (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Czene, E. Toth, E. Nemeth, H. Otten, J. N. Poulsen, H. E. M. Christensen, L. Rulisek, K. Nagata, S. Larsen, B. Gyurcsik
A New Insight Into The Zinc-Dependent Dna-Cleavage By The Colicin E7 Nuclease: A Crystallographic And Computational Study.
Metallomics V. 6 2090 2014
PubMed-ID: 25179124  |  Reference-DOI: 10.1039/C4MT00195H

(-) Compounds

Molecule 1 - COLICIN-E7
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET21A
    Expression System Vector Type: PLASMID
    Fragment: COLICIN E7 METALLONUCLEASE DOMAIN, RESIDUES 450-573
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 469008

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL2Ligand/IonCHLORIDE ION
3SO49Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3SO45Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3SO44Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:544 , HIS A:569 , HIS A:573 , SO4 A:1136BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREHIS B:544 , HIS B:569 , HIS B:573 , SO4 B:1134BINDING SITE FOR RESIDUE ZN B 401
03AC3SOFTWAREGLY A:455 , HOH A:2010 , HOH A:2011 , HOH A:2085BINDING SITE FOR RESIDUE CL A1133
04AC4SOFTWAREGLY B:455 , HOH B:2009 , HOH B:2010 , HOH B:2077BINDING SITE FOR RESIDUE CL B1133
05AC5SOFTWAREARG A:530 , THR A:531 , GLN A:532 , HOH A:2061 , HOH A:2089 , ARG B:530 , THR B:531BINDING SITE FOR RESIDUE SO4 A1134
06AC6SOFTWAREGLY A:451 , GLY A:554 , VAL A:555 , TYR A:556 , HOH A:2005 , HOH A:2092 , ASN B:552BINDING SITE FOR RESIDUE SO4 A1135
07AC7SOFTWAREZN B:401 , LEU B:543 , HIS B:544 , HIS B:545 , HIS B:569 , HIS B:573 , HOH B:2067BINDING SITE FOR RESIDUE SO4 B1134
08AC8SOFTWAREZN A:401 , LEU A:543 , HIS A:544 , HIS A:545 , HIS A:569 , HOH A:2070 , HOH A:2076BINDING SITE FOR RESIDUE SO4 A1136
09AC9SOFTWAREHOH A:2080 , GLY B:554 , VAL B:555 , TYR B:556 , HOH B:2006 , HOH B:2008 , HOH B:2072BINDING SITE FOR RESIDUE SO4 B1135
10BC1SOFTWAREGLN A:532 , SER B:514 , ASN B:516 , HOH B:2051 , HOH B:2052BINDING SITE FOR RESIDUE SO4 B1136
11BC2SOFTWAREARG A:496 , GLU A:542 , LEU A:543 , HOH A:2041 , HOH A:2045 , HOH A:2093BINDING SITE FOR RESIDUE SO4 A1137
12BC3SOFTWAREARG B:496 , GLU B:542 , LEU B:543 , HOH B:2037 , HOH B:2041 , HOH B:2063BINDING SITE FOR RESIDUE SO4 B1137
13BC4SOFTWARESER A:514 , HOH A:2051 , HOH A:2055BINDING SITE FOR RESIDUE SO4 A1138
14BC5SOFTWAREARG B:496 , LYS B:497 , LYS B:525 , HOH B:2055 , HOH B:2056BINDING SITE FOR RESIDUE ACT B1138
15BC6SOFTWAREILE B:549 , SER B:550 , HOH B:2067BINDING SITE FOR RESIDUE ACT B1139

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZFK)

(-) 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:128
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:128
                                   455       465       475       485       495       505       515       525       535       545       555       565        
           CEA7_ECOLX   446 KRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIH 573
               SCOP domains d3zfka_ A: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....................ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee..hhhhh........eeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zfk A 446 SPEFPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIH 573
                                   455       465       475       485       495       505       515       525       535       545       555       565        


Chain B from PDB  Type:PROTEIN  Length:128
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:128
                                   455       465       475       485       495       505       515       525       535       545       555       565        
           CEA7_ECOLX   446 KRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIH 573
               SCOP domains d3zfkb_ B: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....................ee.hhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhh.......eeee..hhhhh........eeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zfk B 446 SPEFPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIH 573
                                   455       465       475       485       495       505       515       525       535       545       555       565
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  3zfk
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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 3fbd 3gjn 3gkl 7cei

(-) Related Entries Specified in the PDB File

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