DB code: S00402

RLCP classification 1.15.8230.371 : Hydrolysis
CATH domain 3.40.570.10 : Extracellular Endonuclease; Chain A Catalytic domain
E.C. 3.1.30.2
CSA 1smn
M-CSA 1smn
MACiE M0042

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Contains Pfam
P13717 Nuclease
EC 3.1.30.2
Endonuclease
Nuclease isoform Sm2
Nuclease isoform Sm3
Nuclease isoform Sm1
PF01223 (Endonuclease_NS)
[Graphical View]

KEGG enzyme name
Serratia marcescens nuclease
endonuclease (Serratia marcescens)
barley nuclease
plant nuclease I
nucleate endonuclease

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P13717 NUCA_SERMA Endonucleolytic cleavage to 5''- phosphomononucleotide and 5''-phosphooligonucleotide end-products. Homodimer. Secreted. Binds 1 magnesium ion.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00046 C00039 C00001 C00171 C00351
E.C.
Compound magnesium RNA DNA H2O 5'-Phosphomononucleotide 5'-Phosphooligonucleotide
Type divalent metal (Ca2+, Mg2+) nucleic acids nucleic acids H2O nucleotide nucleic acids,phosphate group/phosphate ion
ChEBI 18420
15377
PubChem 888
22247451
962
1g8tA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Unbound Unbound
1g8tB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Unbound Unbound
1ql0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ql0B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1smnA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1smnB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qaeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Unbound Unbound
1qaeB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1g8tA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 57;HIS 89;GLU 127 ASN 119(Mg2+ binding)
1g8tB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 57;HIS 89;GLU 127 ASN 119(Mg2+ binding)
1ql0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 57;HIS 89;GLU 127 ASN 119(Mg2+ binding)
1ql0B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 57;HIS 89;GLU 127 ASN 119(Mg2+ binding)
1smnA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 57;HIS 89;GLU 127 ASN 119(Mg2+ binding)
1smnB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 57;HIS 89;GLU 127 ASN 119(Mg2+ binding)
1qaeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 57;HIS 89;GLU 127 ASN 119(Mg2+ binding)
1qaeB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 57;HIS 89;GLU 127 ASN 119(Mg2+ binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.463-466
[4]
Fig.4, p.2637-2639
[5]
Fig.1, p.345-346
[6]
Fig.4 2
[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]
Resource
Comments
Medline ID
PubMed ID 7664065
Journal Nat Struct Biol
Year 1994
Volume 1
Pages 461-8
Authors Miller MD, Tanner J, Alpaugh M, Benedik MJ, Krause KL
Title 2.1 A structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8078761
Journal Nucleic Acids Res
Year 1994
Volume 22
Pages 3280-7
Authors Friedhoff P, Gimadutdinow O, Pingoud A
Title Identification of catalytically relevant amino acids of the extracellular Serratia marcescens endonuclease by alignment-guided mutagenesis.
Related PDB
Related UniProtKB
[3]
Resource
Comments light-scattering experiments, crystal packing analysis
Medline ID
PubMed ID 8771193
Journal Protein Sci
Year 1996
Volume 5
Pages 24-33
Authors Miller MD, Krause KL
Title Identification of the Serratia endonuclease dimer: structural basis and implications for catalysis.
Related PDB 1smn
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8758988
Journal Nucleic Acids Res
Year 1996
Volume 24
Pages 2632-9
Authors Friedhoff P, Kolmes B, Gimadutdinow O, Wende W, Krause KL, Pingoud A
Title Analysis of the mechanism of the Serratia nuclease using site-directed mutagenesis.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8955376
Journal FEBS Lett
Year 1996
Volume 397
Pages 343-6
Authors Kolmes B, Franke I, Friedhoff P, Pingoud A
Title Analysis of the reaction mechanism of the non-specific endonuclease of Serratia marcescens using an artificial minimal substrate.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 9257723
Journal FEBS Lett
Year 1997
Volume 412
Pages 217-22
Authors Lunin VY, Levdikov VM, Shlyapnikov SV, Blagova EV, Lunin VV, Wilson KS, Mikhailov AM
Title Three-dimensional structure of Serratia marcescens nuclease at 1.7 A resolution and mechanism of its action.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9563525
Journal FEBS Lett
Year 1998
Volume 425
Pages 517-22
Authors Franke I, Meiss G, Blecher D, Gimadutdinow O, Urbanke C, Pingoud A
Title Genetic engineering, production and characterisation of monomeric variants of the dimeric Serratia marcescens endonuclease.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9989607
Journal FEBS Lett
Year 1999
Volume 443
Pages 209-14
Authors Friedhoff P, Franke I, Krause KL, Pingoud A
Title Cleavage 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.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 10048918
Journal Nat Struct Biol
Year 1999
Volume 6
Pages 112-3
Authors Friedhoff P, Franke I, Meiss G, Wende W, Krause KL, Pingoud A
Title A similar active site for non-specific and specific endonucleases.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10329148
Journal J Mol Biol
Year 1999
Volume 288
Pages 377-90
Authors Meiss G, Gast FU, Pingoud AM
Title The DNA/RNA non-specific Serratia nuclease prefers double-stranded A-form nucleic acids as substrates.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 10329193
Journal J Mol Biol
Year 1999
Volume 288
Pages 975-87
Authors Miller MD, Cai J, Krause KL
Title The active site of Serratia endonuclease contains a conserved magnesium-water cluster.
Related PDB 1qae
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 10715218
Journal J Mol Biol
Year 2000
Volume 297
Pages 521-34
Authors Meiss G, Gimadutdinow O, Haberland B, Pingoud A
Title Mechanism of DNA cleavage by the DNA/RNA-non-specific Anabaena sp. PCC 7120 endonuclease NucA and its inhibition by NuiA.
Related PDB
Related UniProtKB
[13]
Resource
Comments X-ray crystallography (1.1 Angstroms)
Medline ID
PubMed ID 10771425
Journal Acta Crystallogr D Biol Crystallogr
Year 2000
Volume 56
Pages 567-572
Authors Shlyapnikov SV, Lunin VV, Perbandt M, Polyakov KM, Lunin VY, Levdikov VM, Betzel C, Mikhailov AM
Title Atomic structure of the Serratia marcescens endonuclease at 1.1 A resolution and the enzyme reaction mechanism.
Related PDB 1g8t 1ql0
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11553482
Journal Bioorg Med Chem
Year 2001
Volume 9
Pages 2403-9
Authors Koziolkiewicz M, Owczarek A, Domanski K, Nowak M, Guga P, Stec WJ
Title Stereochemistry of cleavage of internucleotide bonds by Serratia marcescens endonuclease.
Related PDB
Related UniProtKB

Comments
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.
This enzyme belongs to the DNA/RNA non-specific endonuclease family.

Created Updated
2002-09-27 2009-02-26