P13717 (NUCA_SERMA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Nuclease
EC=3.1.30.2

Alternative name(s):
Endonuclease

Cleaved into the following 3 chains:

1. Nuclease isoform Sm2
2. Nuclease isoform Sm3
3. Nuclease isoform Sm1

Gene names

Name:	nucA
Synonyms:	nuc

Organism

Serratia marcescens

Taxonomic identifier

615 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Serratia

Protein attributes

Sequence length	266 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the hydrolysis of both DNA and RNA, double- or single-stranded, at the 3'position of the phosphodiester bond to produce 5'-phosphorylated mono-, di-, tri- and tetranucleotides. DNA is a slightly better substrate than RNA.
Catalytic activity	Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products.
Cofactor	Binds 1 magnesium ion.
Subunit structure	Homodimer. Ref.9
Subcellular location	Secreted.
Miscellaneous	The active site contains 1 hydrated magnesium ion that has only 1 direct interaction with the protein; all other interactions are via water molecules.
Sequence similarities	Belongs to the DNA/RNA non-specific endonuclease family.
Mass spectrometry	Molecular mass is 26708.2 Da from positions 22 - 266. Determined by ESI. Isoform Sm2. Ref.4 Molecular mass is 26591.8 Da from positions 23 - 266. Determined by ESI. Isoform Sm3. Ref.4 Molecular mass is 26376.4 Da from positions 25 - 266. Determined by ESI. Isoform Sm1. Ref.4

Ontologies

Keywords
Cellular component	Secreted
Domain	Signal
Ligand	Magnesium Metal-binding
Molecular function	Endonuclease Hydrolase Nuclease
PTM	Disulfide bond
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC
Cellular_component	extracellular region Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	endonuclease activity Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 21

21

Chain

22 – 266

245

Nuclease isoform Sm2

PRO_0000019914

Chain

23 – 266

244

Nuclease isoform Sm3

PRO_0000019915

Chain

25 – 266

242

Nuclease isoform Sm1

PRO_0000019916

Sites

Active site

110

1

Proton acceptor Ref.5

Metal binding

140

1

Magnesium; catalytic

Amino acid modifications

Disulfide bond

30 ↔ 34

Ref.3 Ref.4

Disulfide bond

222 ↔ 264

Ref.3 Ref.4

Experimental info

Mutagenesis

78

1

R → A: Reduced activity 1000-fold. Ref.7

Mutagenesis

78

1

R → K: Reduced activity 100-fold. Ref.7

Mutagenesis

108

1

R → A: Reduced activity 1000-fold. Ref.7

Mutagenesis

108

1

R → K: Reduced activity 50-fold. Ref.7

Mutagenesis

110

1

H → A, D, E, K or Q: Reduced activity 100000-fold. Ref.7

Mutagenesis

110

1

H → N: Reduced activity 1000-fold. Ref.7

Mutagenesis

140

1

N → A, D or H: Reduced activity over 10000-fold. Ref.7

Mutagenesis

140

1

N → Q: Reduced activity 1000-fold. Ref.7

Mutagenesis

148

1

E → A, D or Q: Reduced activity over 800-fold. Ref.7

Secondary structure

1

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266

Helix Strand Turn

Details...

Beta strand

29 – 32

4

Beta strand

39 – 42

4

Beta strand

50 – 53

4

Turn

55 – 57

3

Beta strand

58 – 67

10

Helix

88 – 90

3

Helix

94 – 97

4

Helix

100 – 104

5

Beta strand

106 – 112

7

Helix

114 – 117

4

Helix

123 – 127

5

Helix

129 – 131

3

Beta strand

132 – 136

5

Helix

137 – 140

4

Helix

143 – 153

11

Helix

154 – 156

3

Beta strand

163 – 170

8

Beta strand

189 – 197

9

Turn

201 – 203

3

Beta strand

206 – 212

7

Helix

221 – 224

4

Helix

228 – 235

8

Beta strand

238 – 240

3

Helix

245 – 252

8

Helix

258 – 262

5

Sequences

	Sequence		Length	Mass (Da)
	P13717 [UniParc]. Last modified February 1, 1996. Version 2. Checksum: A0FF0C1430677B9E	FASTA	266	28,945
	10 20 30 40 50 60 MRFNNKMLAL AALLFAAQAS ADTLESIDNC AVGCPTGGSS NVSIVRHAYT LNNNSTTKFA 70 80 90 100 110 120 NWVAYHITKD TPASGKTRNW KTDPALNPAD TLAPADYTGA NAALKVDRGH QAPLASLAGV 130 140 150 160 170 180 SDWESLNYLS NITPQKSDLN QGAWARLEDQ ERKLIDRADI SSVYTVTGPL YERDMGKLPG 190 200 210 220 230 240 TQKAHTIPSA YWKVIFINNS PAVNHYAAFL FDQNTPKGAD FCQFRVTVDE IEKRTGLIIW 250 260 AGLPDDVQAS LKSKPGVLPE LMGCKN

References

[1]	"The extracellular nuclease gene of Serratia marcescens and its secretion from Escherichia coli." Ball T.K., Saurugger P.N., Benedick M.J. Gene 57:183-192(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: W225.
[2]	Benedick M.J. Submitted (OCT-1989) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION TO 7-11.
[3]	"Purification and characterization of a Serratia marcescens nuclease produced by Escherichia coli." Biedermann K., Jepsen P.K., Riise E., Svendsen I. Carlsberg Res. Commun. 54:17-27(1989) [PubMed] [Europe PMC] [Abstract] Cited for: PARTIAL PROTEIN SEQUENCE, DISULFIDE BONDS.
[4]	"Characterization of Serratia marcescens nuclease isoforms by plasma desorption mass spectrometry." Pedersen J., Filimonova M.N., Roepstorff P., Biedermann K. Biochim. Biophys. Acta 1202:13-21(1993) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION OF ISOFORMS SM1; SM2 AND SM3, MASS SPECTROMETRY, DISULFIDE BONDS. Strain: B10M1.
[5]	"Identification of catalytically relevant amino acids of the extracellular Serratia marcescens endonuclease by alignment-guided mutagenesis." Friedhoff P., Gimadutdinow O., Pingoud A. Nucleic Acids Res. 22:3280-3287(1994) [PubMed] [Europe PMC] [Abstract] Cited for: ACTIVE SITE.
[6]	"Kinetic studies of the Serratia marcescens extracellular nuclease isoforms." Filimonova M.N., Krause K.L., Benedik M.J. Biochem. Mol. Biol. Int. 33:1229-1236(1994) [PubMed] [Europe PMC] [Abstract] Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
[7]	"Analysis of the mechanism of the Serratia nuclease using site-directed mutagenesis." Friedhoff P., Kolmes B., Gimadutdinow O., Wende W., Krause K.L., Pingoud A. Nucleic Acids Res. 24:2632-2639(1996) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ARG-78; ARG-108; HIS-110; ASN-140 AND GLU-148.
[8]	"Serratia marcescens and its extracellular nuclease." Benedik M.J., Strych U. FEMS Microbiol. Lett. 165:1-13(1998) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW.
[9]	"2.1-A structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA." Miller M.D., Tanner J., Alpaugh M., Benedik M.J., Krause K.L. Nat. Struct. Biol. 1:461-468(1994) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH MAGNESIUM IONS, SUBUNIT.
[10]	"Three-dimensional structure of Serratia marcescens nuclease at 1.7-A resolution and mechanism of its action." Lunin V.Y., Levdikov V.M., Shlyapnikov S.V., Blagova E.V., Lunin V.V., Wilson K.S., Mikhailov A.M. FEBS Lett. 412:217-222(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
[11]	"Atomic structure of the Serratia marcescens endonuclease at 1.1 A resolution and the enzyme reaction mechanism." Shlyapnikov S.V., Lunin V.V., Perbandt M., Polyakov K.M., Lunin V.Y., Levdikov V.M., Betzel C., Mikhailov A.M. Acta Crystallogr. D 56:567-572(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.1 ANGSTROMS) OF 22-266 IN COMPLEX WITH MAGNESIUM IONS.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M19495 Genomic DNA. Translation: AAA26560.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1G8T	X-ray	1.10	A/B	22-266	[»]
1QAE	X-ray	2.05	A/B	22-266	[»]
1QL0	X-ray	1.10	A/B	26-266	[»]
1SMN	X-ray	2.04	A/B	22-266	[»]

ProteinModelPortal

P13717.

SMR

P13717. Positions 26-266.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

3.40.570.10. 1 hit.

InterPro

IPR018524. DNA/RNA_endonuclease_AS.
IPR001604. DNA/RNA_non-sp_Endonuclease.
IPR020821. Extracellular_endonuc_su_A.
[Graphical view]

Pfam

PF01223. Endonuclease_NS. 1 hit.
[Graphical view]

SMART

SM00892. Endonuclease_NS. 1 hit.
SM00477. NUC. 1 hit.
[Graphical view]

PROSITE

PS01070. NUCLEASE_NON_SPEC. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P13717.

Entry information

Entry name

NUCA_SERMA

Accession

Primary (citable) accession number: P13717

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	February 1, 1996
Last modified:	April 3, 2013
This is version 91 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program