EzCatDB: S00402

DB codeS00402
RLCP classification1.15.8230.371
CATH domainDomain 13.40.570.10Catalytic domain
E.C.3.1.30.2
CSA1smn
MACiEM0042


Enzyme Name
Swiss-protKEGG

P13717
Protein nameNucleaseSerratia marcescens nuclease
endonuclease (Serratia marcescens)
barley nuclease
plant nuclease I
nucleate endonuclease
SynonymsEC 3.1.30.2
Endonuclease
ContainsNuclease isoform Sm2
Nuclease isoform Sm3
Nuclease isoform Sm1


Swiss-prot:Accession NumberP13717
Entry nameNUCA_SERMA
ActivityEndonucleolytic cleavage to 5''- phosphomononucleotide and 5''-phosphooligonucleotide end-products.
SubunitHomodimer.
Subcellular locationSecreted.
CofactorBinds 1 magnesium ion.


CofactorsSubstratesProducts
KEGG-idC00305C00046C00039C00001C00171C00351
CompoundmagnesiumRNADNAH2O5'-Phosphomononucleotide5'-Phosphooligonucleotide
Typedivalent metal (Ca2+, Mg2+)nucleic acidsnucleic acidsH2Onucleotidenucleic acids,phosphate group/phosphate ion
1g8tABound:_MGUnboundUnbound
UnboundUnbound
1g8tBBound:_MGUnboundUnbound
UnboundUnbound
1ql0AUnboundUnboundUnbound
UnboundUnbound
1ql0BUnboundUnboundUnbound
UnboundUnbound
1smnAUnboundUnboundUnbound
UnboundUnbound
1smnBUnboundUnboundUnbound
UnboundUnbound
1qaeABound:_MGUnboundUnbound
UnboundUnbound
1qaeBBound:_MGUnboundUnbound
UnboundUnbound

Active-site residues
pdbCatalytic residuesModified residues
1g8tAARG 57;HIS 89;GLU 127
ASN 119(Mg2+ binding)
1g8tBARG 57;HIS 89;GLU 127
ASN 119(Mg2+ binding)
1ql0AARG 57;HIS 89;GLU 127
ASN 119(Mg2+ binding)
1ql0BARG 57;HIS 89;GLU 127
ASN 119(Mg2+ binding)
1smnAARG 57;HIS 89;GLU 127
ASN 119(Mg2+ binding)
1smnBARG 57;HIS 89;GLU 127
ASN 119(Mg2+ binding)
1qaeAARG 57;HIS 89;GLU 127
ASN 119(Mg2+ binding)
1qaeBARG 57;HIS 89;GLU 127
ASN 119(Mg2+ binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]p.463-466
[4]Fig.4, p.2637-2639
[5]Fig.1, p.345-346
[6]Fig.42
[8]Fig.3, p.212-213
[11]Fig.3, Fig.6, p.983
[13]Fig.3, p.569-572
[14]Fig.1, p.2407-2408

references
[1]
PubMed ID7664065
JournalNat Struct Biol
Year1994
Volume1
Pages461-8
AuthorsMiller MD, Tanner J, Alpaugh M, Benedik MJ, Krause KL
Title2.1 A structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA.
[2]
PubMed ID8078761
JournalNucleic Acids Res
Year1994
Volume22
Pages3280-7
AuthorsFriedhoff P, Gimadutdinow O, Pingoud A
TitleIdentification of catalytically relevant amino acids of the extracellular Serratia marcescens endonuclease by alignment-guided mutagenesis.
[3]
Commentslight-scattering experiments, crystal packing analysis
PubMed ID8771193
JournalProtein Sci
Year1996
Volume5
Pages24-33
AuthorsMiller MD, Krause KL
TitleIdentification of the Serratia endonuclease dimer: structural basis and implications for catalysis.
Related PDB1smn
[4]
PubMed ID8758988
JournalNucleic Acids Res
Year1996
Volume24
Pages2632-9
AuthorsFriedhoff P, Kolmes B, Gimadutdinow O, Wende W, Krause KL, Pingoud A
TitleAnalysis of the mechanism of the Serratia nuclease using site-directed mutagenesis.
[5]
PubMed ID8955376
JournalFEBS Lett
Year1996
Volume397
Pages343-6
AuthorsKolmes B, Franke I, Friedhoff P, Pingoud A
TitleAnalysis of the reaction mechanism of the non-specific endonuclease of Serratia marcescens using an artificial minimal substrate.
[6]
PubMed ID9257723
JournalFEBS Lett
Year1997
Volume412
Pages217-22
AuthorsLunin VY, Levdikov VM, Shlyapnikov SV, Blagova EV, Lunin VV, Wilson KS, Mikhailov AM
TitleThree-dimensional structure of Serratia marcescens nuclease at 1.7 A resolution and mechanism of its action.
[7]
PubMed ID9563525
JournalFEBS Lett
Year1998
Volume425
Pages517-22
AuthorsFranke I, Meiss G, Blecher D, Gimadutdinow O, Urbanke C, Pingoud A
TitleGenetic engineering, production and characterisation of monomeric variants of the dimeric Serratia marcescens endonuclease.
[8]
PubMed ID9989607
JournalFEBS Lett
Year1999
Volume443
Pages209-14
AuthorsFriedhoff P, Franke I, Krause KL, Pingoud A
TitleCleavage experiments with deoxythymidine 3',5'-bis-(p-nitrophenyl phosphate) suggest that the homing endonuclease I-PpoI follows the same mechanism of phosphodiester bond hydrolysis as the non-specific Serratia nuclease.
[9]
PubMed ID10048918
JournalNat Struct Biol
Year1999
Volume6
Pages112-3
AuthorsFriedhoff P, Franke I, Meiss G, Wende W, Krause KL, Pingoud A
TitleA similar active site for non-specific and specific endonucleases.
[10]
PubMed ID10329148
JournalJ Mol Biol
Year1999
Volume288
Pages377-90
AuthorsMeiss G, Gast FU, Pingoud AM
TitleThe DNA/RNA non-specific Serratia nuclease prefers double-stranded A-form nucleic acids as substrates.
[11]
PubMed ID10329193
JournalJ Mol Biol
Year1999
Volume288
Pages975-87
AuthorsMiller MD, Cai J, Krause KL
TitleThe active site of Serratia endonuclease contains a conserved magnesium-water cluster.
Related PDB1qae
[12]
PubMed ID10715218
JournalJ Mol Biol
Year2000
Volume297
Pages521-34
AuthorsMeiss G, Gimadutdinow O, Haberland B, Pingoud A
TitleMechanism of DNA cleavage by the DNA/RNA-non-specific Anabaena sp. PCC 7120 endonuclease NucA and its inhibition by NuiA.
[13]
CommentsX-ray crystallography (1.1 Angstroms)
PubMed ID10771425
JournalActa Crystallogr D Biol Crystallogr
Year2000
Volume56
Pages567-572
AuthorsShlyapnikov SV, Lunin VV, Perbandt M, Polyakov KM, Lunin VY, Levdikov VM, Betzel C, Mikhailov AM
TitleAtomic structure of the Serratia marcescens endonuclease at 1.1 A resolution and the enzyme reaction mechanism.
Related PDB1g8t,1ql0
[14]
PubMed ID11553482
JournalBioorg Med Chem
Year2001
Volume9
Pages2403-9
AuthorsKoziolkiewicz M, Owczarek A, Domanski K, Nowak M, Guga P, Stec WJ
TitleStereochemistry of cleavage of internucleotide bonds by Serratia marcescens endonuclease.

comments
This enzyme belongs to the DNA/RNA non-specific endonuclease family.
To date, several catalytic mechanisms have been proposed. In the early study, a simple acid/base mechanism, in which His89 acts as a general acid and Glu127 serves as either a nucleophile or a general base, activating a water molecule, has been proposed [1], [6]. However, in more recent years, the two catalytic mechanisms have been proposed. In both the mechanisms, Asn119 binds directly to the divalent metal, Mg2+, whilst Glu127 contacts the water cluster coordinating the magnesium, and Arg57 can stabilize the transition state of the phosphate. There are some differences in these two mechanisms, as follows:
(1) An unligated solvent water molecule is activated directly by the general base, His89, and then attacks the phosphorous atom as a nucleophile. Two phosphate oxygen atoms, including 3'-bridging oxygen, are bound to the magnesium. (see [8], [14])
(2) A magnesium-bound water is activated by the general base, His89, and becomes the attacking nucleophile. The 3'-bridging oxygen is bound to the magnesium. (see [13])
It is still not clear which mechanism is correct, without 3D-structure with the cognate substrate molecule. However, considering the structure with sulfate ion, which mimics the scissile phosphoric ester bond, the option (1) is more likely.

createdupdated
2002-09-272009-02-26


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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