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 18420			15377 15377
PubChem	888 888			22247451 962 22247451 962

1g8tA	Bound:_MG	Unbound	Unbound		Unbound	Unbound
1g8tB	Bound:_MG	Unbound	Unbound		Unbound	Unbound
1ql0A	Unbound	Unbound	Unbound		Unbound	Unbound
1ql0B	Unbound	Unbound	Unbound		Unbound	Unbound
1smnA	Unbound	Unbound	Unbound		Unbound	Unbound
1smnB	Unbound	Unbound	Unbound		Unbound	Unbound
1qaeA	Bound:_MG	Unbound	Unbound		Unbound	Unbound
1qaeB	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	ARG 57;HIS 89;GLU 127		ASN 119(Mg2+ binding)
1g8tB	ARG 57;HIS 89;GLU 127		ASN 119(Mg2+ binding)
1ql0A	ARG 57;HIS 89;GLU 127		ASN 119(Mg2+ binding)
1ql0B	ARG 57;HIS 89;GLU 127		ASN 119(Mg2+ binding)
1smnA	ARG 57;HIS 89;GLU 127		ASN 119(Mg2+ binding)
1smnB	ARG 57;HIS 89;GLU 127		ASN 119(Mg2+ binding)
1qaeA	ARG 57;HIS 89;GLU 127		ASN 119(Mg2+ binding)
1qaeB	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.

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