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P13717 (NUCA_SERMA) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 94. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Nuclease

EC=3.1.30.2
Alternative name(s):
Endonuclease
Gene names
Name:nucA
Synonyms:nuc
OrganismSerratia marcescens
Taxonomic identifier615 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSerratia

Protein attributes

Sequence length266 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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 componentSecreted
   DomainSignal
   LigandMagnesium
Metal-binding
   Molecular functionEndonuclease
Hydrolase
Nuclease
   PTMDisulfide bond
   Technical term3D-structure
Direct protein sequencing
Gene Ontology (GO)
   Cellular_componentextracellular region

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionendonuclease 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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2121
Chain22 – 266245Nuclease isoform Sm2
PRO_0000019914
Chain23 – 266244Nuclease isoform Sm3
PRO_0000019915
Chain25 – 266242Nuclease isoform Sm1
PRO_0000019916

Sites

Active site1101Proton acceptor Ref.5
Metal binding1401Magnesium; catalytic

Amino acid modifications

Disulfide bond30 ↔ 34 Ref.3 Ref.4
Disulfide bond222 ↔ 264 Ref.3 Ref.4

Experimental info

Mutagenesis781R → A: Reduced activity 1000-fold. Ref.7
Mutagenesis781R → K: Reduced activity 100-fold. Ref.7
Mutagenesis1081R → A: Reduced activity 1000-fold. Ref.7
Mutagenesis1081R → K: Reduced activity 50-fold. Ref.7
Mutagenesis1101H → A, D, E, K or Q: Reduced activity 100000-fold. Ref.7
Mutagenesis1101H → N: Reduced activity 1000-fold. Ref.7
Mutagenesis1401N → A, D or H: Reduced activity over 10000-fold. Ref.7
Mutagenesis1401N → Q: Reduced activity 1000-fold. Ref.7
Mutagenesis1481E → A, D or Q: Reduced activity over 800-fold. Ref.7

Secondary structure

............................................... 266
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P13717 [UniParc].

Last modified February 1, 1996. Version 2.
Checksum: A0FF0C1430677B9E

FASTA26628,945
        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 

« Hide

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
EntryMethodResolution (Å)ChainPositionsPDBsum
1G8TX-ray1.10A/B22-266[»]
1QAEX-ray2.05A/B22-266[»]
1QL0X-ray1.10A/B26-266[»]
1SMNX-ray2.04A/B22-266[»]
4E3YX-ray0.95A/B22-266[»]
ProteinModelPortalP13717.
SMRP13717. Positions 26-266.
ModBaseSearch...
MobiDBSearch...

Proteomic databases

PRIDEP13717.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D3.40.570.10. 1 hit.
InterProIPR018524. DNA/RNA_endonuclease_AS.
IPR001604. DNA/RNA_non-sp_Endonuclease.
IPR020821. Extracellular_endonuc_su_A.
[Graphical view]
PfamPF01223. Endonuclease_NS. 1 hit.
[Graphical view]
SMARTSM00892. Endonuclease_NS. 1 hit.
SM00477. NUC. 1 hit.
[Graphical view]
PROSITEPS01070. NUCLEASE_NON_SPEC. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP13717.

Entry information

Entry nameNUCA_SERMA
AccessionPrimary (citable) accession number: P13717
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: February 1, 1996
Last modified: April 16, 2014
This is version 94 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references