EzCatDB: D00157

DB codeD00157
CATH domainDomain 1-.-.-.-
Domain 23.90.540.10Catalytic domain
E.C.3.1.-.-
CSA1fr2


Enzyme Name
Swiss-prot

P09883
Protein nameColicin-E9
SynonymsEC 3.1.-.-


Swiss-prot:Accession NumberP09883
Entry nameCEA9_ECOLX
Activity
Subunit
Subcellular location
Cofactor


CofactorsSubstratesProducts
KEGG-idC00038C00039C00434C00001C00351C03236
CompoundZincDNADouble-stranded DNAH2O5'-Phosphooligonucleotide5'-Phosphodinucleotide
Typeheavy metalnucleic acidsnucleic acidsH2Onucleic acids,phosphate group/phosphate ionnucleic acids,phosphate group/phosphate ion
1bxiBAnalogue:_NIUnboundUnbound
UnboundUnbound
1emvBUnboundUnboundUnbound
UnboundUnbound
1fr2BBound:_ZNUnboundUnbound
UnboundUnbound
1fsjBBound:_ZNUnboundUnbound
UnboundUnbound
1fsjCBound:_ZNUnboundUnbound
UnboundUnbound
1fsjDBound:_ZNUnboundUnbound
UnboundUnbound
1fsjEBound:_ZNUnboundUnbound
UnboundUnbound

Active-site residues
resource
Swiss-prot;P09883 & literature [17]
pdbCatalytic residuesModified residues
1bxiBHIS 103
HIS 102;HIS 127;HIS 131(zinc binding)
1emvBHIS 103
HIS 102;HIS 127;HIS 131(zinc binding)
1fr2BHIS 103
HIS 102;HIS 127;HIS 131(zinc binding)
1fsjBHIS 103
HIS 102;HIS 127;HIS 131(zinc binding)
1fsjCHIS 303
HIS 302;HIS 327;HIS 331(zinc binding)
1fsjDHIS 503
HIS 502;HIS 527;HIS 531(zinc binding)
1fsjEHIS 703
HIS 702;HIS 727;HIS 731(zinc binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[17]Fig.4, p.9292

references
[1]
PubMed ID8709151
JournalJ Mol Biol
Year1996
Volume260
Pages731-42
AuthorsGarinot-Schneider C, Pommer AJ, Moore GR, Kleanthous C, James R
TitleIdentification of putative active-site residues in the DNase domain of colicin E9 by random mutagenesis.
[2]
PubMed ID9169618
JournalBiochem J
Year1997
Volume323
Pages823-31
AuthorsOsborne MJ, Wallis R, Leung KY, Williams G, Lian LY, James R, Kleanthous C, Moore GR
TitleIdentification of critical residues in the colicin E9 DNase binding region of the Im9 protein.
[3]
PubMed ID9716496
JournalBiochem J
Year1998
Volume334
Pages387-92
AuthorsPommer AJ, Wallis R, Moore GR, James R, Kleanthous C
TitleEnzymological characterization of the nuclease domain from the bacterial toxin colicin E9 from Escherichia coli.
[4]
PubMed ID9718299
JournalBiochemistry
Year1998
Volume37
Pages11771-9
AuthorsLi W, Hamill SJ, Hemmings AM, Moore GR, James R, Kleanthous C
TitleDual recognition and the role of specificity-determining residues in colicin E9 DNase-immunity protein interactions.
[5]
PubMed ID9425068
JournalBiochemistry
Year1998
Volume37
Pages476-85
AuthorsWallis R, Leung KY, Osborne MJ, James R, Moore GR, Kleanthous C
TitleSpecificity in protein-protein recognition: conserved Im9 residues are the major determinants of stability in the colicin E9 DNase-Im9 complex.
[6]
PubMed ID9917143
JournalJ Biomol NMR
Year1998
Volume12
Pages567-8
AuthorsBoetzel R, Czisch M, MacDonald CJ, Kaptein R, Hemmings AM, James R, Kleanthous C, Moore GR
TitleAssignment of 1H, 13C and 15N signals of the inhibitor protein Im9 bound to the DNase domain of colicin E9.
[7]
PubMed ID9729794
JournalJ Biomol NMR
Year1998
Volume12
Pages145-59
AuthorsWhittaker SB, Boetzel R, MacDonald C, Lian LY, Pommer AJ, Reilly A, James R, Kleanthous C, Moore GR
TitleNMR detection of slow conformational dynamics in an endonuclease toxin.
[8]
PubMed ID10480931
JournalJ Biol Chem
Year1999
Volume274
Pages27153-60
AuthorsPommer AJ, Kuhlmann UC, Cooper A, Hemmings AM, Moore GR, James R, Kleanthous C
TitleHoming in on the role of transition metals in the HNH motif of colicin endonucleases.
[9]
PubMed ID10610142
JournalJ Biomol NMR
Year1999
Volume14
Pages201-2
AuthorsWhittaker SB, Boetzel R, MacDonald C, Lian LY, James R, Kleanthous C, Moore GR
TitleAssignment of 1H, 13C and 15N signals of the DNase domain of colicin E9.
[10]
PubMed ID10677364
JournalBiochem J
Year2000
Volume346 Pt 2
Pages441-5
AuthorsHo TY, Wu SL, Hsiang CH, Chang TJ, Hsiang CY
TitleIdentification of a DNA-binding domain and an active-site residue of pseudorabies virus DNase.
[11]
CommentsX-ray crystallography
PubMed ID10966813
JournalJ Mol Biol
Year2000
Volume301
Pages1163-78
AuthorsKuhlmann UC, Pommer AJ, Moore GR, James R, Kleanthous C
TitleSpecificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes.
Related PDB1emv,1bxi
[12]
PubMed ID11045617
JournalProtein Sci
Year2000
Volume9
Pages1709-18
AuthorsBoetzel R, Czisch M, Kaptein R, Hemmings AM, James R, Kleanthous C, Moore GR
TitleNMR investigation of the interaction of the inhibitor protein Im9 with its partner DNase.
[13]
PubMed ID10794413
JournalProtein Sci
Year2000
Volume9
Pages713-20
AuthorsWhittaker SB, Czisch M, Wechselberger R, Kaptein R, Hemmings AM, James R, Kleanthous C, Moore GR
TitleSlow conformational dynamics of an endonuclease persist in its complex with its natural protein inhibitor.
[14]
PubMed ID12162738
JournalBiochemistry
Year2002
Volume41
Pages10234-44
AuthorsKeeble AH, Hemmings AM, James R, Moore GR, Kleanthous C
TitleMultistep binding of transition metals to the H-N-H endonuclease toxin colicin E9.
[15]
PubMed ID12021774
JournalNat Struct Biol
Year2002
Volume9
Pages476-84
AuthorsMosbahi K, Lemaitre C, Keeble AH, Mobasheri H, Morel B, James R, Moore GR, Lea EJ, Kleanthous C
TitleThe cytotoxic domain of colicin E9 is a channel-forming endonuclease.
[16]
PubMed ID11884629
JournalNucleic Acids Res
Year2002
Volume30
Pages1325-32
AuthorsKorn C, Scholz SR, Gimadutdinow O, Pingoud A, Meiss G
TitleInvolvement of conserved histidine, lysine and tyrosine residues in the mechanism of DNA cleavage by the caspase-3 activated DNase CAD.
[17]
PubMed ID12899615
JournalBiochemistry
Year2003
Volume42
Pages9288-94
AuthorsScholz SR, Korn C, Bujnicki JM, Gimadutdinow O, Pingoud A, Meiss G
TitleExperimental evidence for a beta beta alpha-Me-finger nuclease motif to represent the active site of the caspase-activated DNase.
[18]
PubMed ID15065879
JournalBiochemistry
Year2004
Volume43
Pages4347-55
Authorsvan den Bremer ET, Keeble AH, Visser AJ, van Hoek A, Kleanthous C, Heck AJ, Jiskoot W
TitleLigand-induced changes in the conformational dynamics of a bacterial cytotoxic endonuclease.

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].

createdupdated
2004-08-182009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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