DB code: D00157

CATH domain -.-.-.- :
3.90.540.10 : Colicin E7 immunity protein; Chain B, fragment Catalytic domain
E.C. 3.1.-.-
CSA 1fr2
M-CSA 1fr2
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P09883 Colicin-E9
EC 3.1.-.-
YP_002533537.1 (Protein)
NC_011977.1 (DNA/RNA sequence)
PF03515 (Cloacin)
PF12639 (Colicin-DNase)
PF11570 (E2R135)
[Graphical View]

KEGG enzyme name

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P09883 CEA9_ECOLX

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C00039 C00434 C00001 C00351 C03236
E.C.
Compound Zinc DNA Double-stranded DNA H2O 5'-Phosphooligonucleotide 5'-Phosphodinucleotide
Type heavy metal nucleic acids nucleic acids H2O nucleic acids,phosphate group/phosphate ion nucleic acids,phosphate group/phosphate ion
ChEBI 29105
15377
PubChem 32051
22247451
962
1bxiB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:_NI Unbound Unbound Unbound Unbound
1emvB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1fr2B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound
1fsjB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound
1fsjC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound
1fsjD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound
1fsjE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P09883 & literature [17]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bxiB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 103 HIS 102;HIS 127;HIS 131(zinc binding)
1emvB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 103 HIS 102;HIS 127;HIS 131(zinc binding)
1fr2B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 103 HIS 102;HIS 127;HIS 131(zinc binding)
1fsjB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 103 HIS 102;HIS 127;HIS 131(zinc binding)
1fsjC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 303 HIS 302;HIS 327;HIS 331(zinc binding)
1fsjD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 503 HIS 502;HIS 527;HIS 531(zinc binding)
1fsjE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 703 HIS 702;HIS 727;HIS 731(zinc binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[17]
Fig.4, p.9292

References
[1]
Resource
Comments
Medline ID
PubMed ID 8709151
Journal J Mol Biol
Year 1996
Volume 260
Pages 731-42
Authors Garinot-Schneider C, Pommer AJ, Moore GR, Kleanthous C, James R
Title Identification of putative active-site residues in the DNase domain of colicin E9 by random mutagenesis.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 9169618
Journal Biochem J
Year 1997
Volume 323
Pages 823-31
Authors Osborne MJ, Wallis R, Leung KY, Williams G, Lian LY, James R, Kleanthous C, Moore GR
Title Identification of critical residues in the colicin E9 DNase binding region of the Im9 protein.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 9716496
Journal Biochem J
Year 1998
Volume 334
Pages 387-92
Authors Pommer AJ, Wallis R, Moore GR, James R, Kleanthous C
Title Enzymological characterization of the nuclease domain from the bacterial toxin colicin E9 from Escherichia coli.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9718299
Journal Biochemistry
Year 1998
Volume 37
Pages 11771-9
Authors Li W, Hamill SJ, Hemmings AM, Moore GR, James R, Kleanthous C
Title Dual recognition and the role of specificity-determining residues in colicin E9 DNase-immunity protein interactions.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 9425068
Journal Biochemistry
Year 1998
Volume 37
Pages 476-85
Authors Wallis R, Leung KY, Osborne MJ, James R, Moore GR, Kleanthous C
Title Specificity in protein-protein recognition: conserved Im9 residues are the major determinants of stability in the colicin E9 DNase-Im9 complex.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 9917143
Journal J Biomol NMR
Year 1998
Volume 12
Pages 567-8
Authors Boetzel R, Czisch M, MacDonald CJ, Kaptein R, Hemmings AM, James R, Kleanthous C, Moore GR
Title Assignment of 1H, 13C and 15N signals of the inhibitor protein Im9 bound to the DNase domain of colicin E9.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9729794
Journal J Biomol NMR
Year 1998
Volume 12
Pages 145-59
Authors Whittaker SB, Boetzel R, MacDonald C, Lian LY, Pommer AJ, Reilly A, James R, Kleanthous C, Moore GR
Title NMR detection of slow conformational dynamics in an endonuclease toxin.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 10480931
Journal J Biol Chem
Year 1999
Volume 274
Pages 27153-60
Authors Pommer AJ, Kuhlmann UC, Cooper A, Hemmings AM, Moore GR, James R, Kleanthous C
Title Homing in on the role of transition metals in the HNH motif of colicin endonucleases.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 10610142
Journal J Biomol NMR
Year 1999
Volume 14
Pages 201-2
Authors Whittaker SB, Boetzel R, MacDonald C, Lian LY, James R, Kleanthous C, Moore GR
Title Assignment of 1H, 13C and 15N signals of the DNase domain of colicin E9.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10677364
Journal Biochem J
Year 2000
Volume 346 Pt 2
Pages 441-5
Authors Ho TY, Wu SL, Hsiang CH, Chang TJ, Hsiang CY
Title Identification of a DNA-binding domain and an active-site residue of pseudorabies virus DNase.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10966813
Journal J Mol Biol
Year 2000
Volume 301
Pages 1163-78
Authors Kuhlmann UC, Pommer AJ, Moore GR, James R, Kleanthous C
Title Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes.
Related PDB 1emv 1bxi
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 11045617
Journal Protein Sci
Year 2000
Volume 9
Pages 1709-18
Authors Boetzel R, Czisch M, Kaptein R, Hemmings AM, James R, Kleanthous C, Moore GR
Title NMR investigation of the interaction of the inhibitor protein Im9 with its partner DNase.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 10794413
Journal Protein Sci
Year 2000
Volume 9
Pages 713-20
Authors Whittaker SB, Czisch M, Wechselberger R, Kaptein R, Hemmings AM, James R, Kleanthous C, Moore GR
Title Slow conformational dynamics of an endonuclease persist in its complex with its natural protein inhibitor.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 12162738
Journal Biochemistry
Year 2002
Volume 41
Pages 10234-44
Authors Keeble AH, Hemmings AM, James R, Moore GR, Kleanthous C
Title Multistep binding of transition metals to the H-N-H endonuclease toxin colicin E9.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 12021774
Journal Nat Struct Biol
Year 2002
Volume 9
Pages 476-84
Authors Mosbahi K, Lemaitre C, Keeble AH, Mobasheri H, Morel B, James R, Moore GR, Lea EJ, Kleanthous C
Title The cytotoxic domain of colicin E9 is a channel-forming endonuclease.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11884629
Journal Nucleic Acids Res
Year 2002
Volume 30
Pages 1325-32
Authors Korn C, Scholz SR, Gimadutdinow O, Pingoud A, Meiss G
Title Involvement of conserved histidine, lysine and tyrosine residues in the mechanism of DNA cleavage by the caspase-3 activated DNase CAD.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 12899615
Journal Biochemistry
Year 2003
Volume 42
Pages 9288-94
Authors Scholz SR, Korn C, Bujnicki JM, Gimadutdinow O, Pingoud A, Meiss G
Title Experimental evidence for a beta beta alpha-Me-finger nuclease motif to represent the active site of the caspase-activated DNase.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 15065879
Journal Biochemistry
Year 2004
Volume 43
Pages 4347-55
Authors van den Bremer ET, Keeble AH, Visser AJ, van Hoek A, Kleanthous C, Heck AJ, Jiskoot W
Title Ligand-induced changes in the conformational dynamics of a bacterial cytotoxic endonuclease.
Related PDB
Related UniProtKB

Comments
This protein is composed of several domains. The PDB structures in this entry correspond to the C-terminal domain of this protein (Swiss-prot;P09883), which seems to be the catalytic domain (see [8], [17]).
Currently, some PDB structures have 1emv no E.C. number, and P09883 of Swiss-prot is classified in E.C. 3.1.-.-.
According to the literature [8], a metal ion, either zinc ion or nickel ion, is nessasary for this protein. However, it does not seem to be involved in catalysis. It seems to play a role in structure stability.
The catalytic mechanism of its homologous enzyme has been discussed in the literature [17].

Created Updated
2004-08-18 2009-02-26