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P13717

- NUCA_SERMA

UniProt

P13717 - NUCA_SERMA

Protein

Nuclease

Gene

nucA

Organism
Serratia marcescens
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 96 (01 Oct 2014)
      Sequence version 2 (01 Feb 1996)
      Previous versions | rss
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    Functioni

    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 activityi

    Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products.PROSITE-ProRule annotation

    Cofactori

    Binds 1 magnesium ion.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei110 – 1101Proton acceptor1 PublicationPROSITE-ProRule annotation
    Metal bindingi140 – 1401Magnesium; catalytic

    GO - Molecular functioni

    1. endonuclease activity Source: UniProtKB-KW
    2. metal ion binding Source: UniProtKB-KW
    3. nucleic acid binding Source: InterPro

    Keywords - Molecular functioni

    Endonuclease, Hydrolase, Nuclease

    Keywords - Ligandi

    Magnesium, Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Nuclease (EC:3.1.30.2)
    Alternative name(s):
    Endonuclease
    Cleaved into the following 3 chains:
    Gene namesi
    Name:nucA
    Synonyms:nuc
    OrganismiSerratia marcescens
    Taxonomic identifieri615 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSerratia

    Subcellular locationi

    GO - Cellular componenti

    1. extracellular region Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Secreted

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi78 – 781R → A: Reduced activity 1000-fold. 1 Publication
    Mutagenesisi78 – 781R → K: Reduced activity 100-fold. 1 Publication
    Mutagenesisi108 – 1081R → A: Reduced activity 1000-fold. 1 Publication
    Mutagenesisi108 – 1081R → K: Reduced activity 50-fold. 1 Publication
    Mutagenesisi110 – 1101H → A, D, E, K or Q: Reduced activity 100000-fold. 1 Publication
    Mutagenesisi110 – 1101H → N: Reduced activity 1000-fold. 1 Publication
    Mutagenesisi140 – 1401N → A, D or H: Reduced activity over 10000-fold. 1 Publication
    Mutagenesisi140 – 1401N → Q: Reduced activity 1000-fold. 1 Publication
    Mutagenesisi148 – 1481E → A, D or Q: Reduced activity over 800-fold. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2121Add
    BLAST
    Chaini22 – 266245Nuclease isoform Sm2PRO_0000019914Add
    BLAST
    Chaini23 – 266244Nuclease isoform Sm3PRO_0000019915Add
    BLAST
    Chaini25 – 266242Nuclease isoform Sm1PRO_0000019916Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi30 ↔ 34
    Disulfide bondi222 ↔ 264

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PRIDEiP13717.

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Structurei

    Secondary structure

    1
    266
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi29 – 324
    Beta strandi39 – 424
    Beta strandi50 – 534
    Turni55 – 573
    Beta strandi58 – 6710
    Helixi88 – 903
    Helixi94 – 974
    Helixi100 – 1045
    Beta strandi106 – 1127
    Helixi114 – 1174
    Helixi123 – 1275
    Helixi129 – 1313
    Beta strandi132 – 1365
    Helixi137 – 1404
    Helixi143 – 15311
    Helixi154 – 1563
    Beta strandi163 – 1708
    Beta strandi189 – 1979
    Turni201 – 2033
    Beta strandi206 – 2127
    Helixi221 – 2244
    Helixi228 – 2358
    Beta strandi238 – 2403
    Helixi245 – 2517
    Helixi258 – 2614

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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[»]
    ProteinModelPortaliP13717.
    SMRiP13717. Positions 26-266.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP13717.

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Signal

    Family and domain databases

    Gene3Di3.40.570.10. 1 hit.
    InterProiIPR018524. DNA/RNA_endonuclease_AS.
    IPR001604. DNA/RNA_non-sp_Endonuclease.
    IPR020821. Extracellular_endonuc_su_A.
    [Graphical view]
    PfamiPF01223. Endonuclease_NS. 1 hit.
    [Graphical view]
    SMARTiSM00892. Endonuclease_NS. 1 hit.
    SM00477. NUC. 1 hit.
    [Graphical view]
    PROSITEiPS01070. NUCLEASE_NON_SPEC. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P13717-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRFNNKMLAL AALLFAAQAS ADTLESIDNC AVGCPTGGSS NVSIVRHAYT    50
    LNNNSTTKFA NWVAYHITKD TPASGKTRNW KTDPALNPAD TLAPADYTGA 100
    NAALKVDRGH QAPLASLAGV SDWESLNYLS NITPQKSDLN QGAWARLEDQ 150
    ERKLIDRADI SSVYTVTGPL YERDMGKLPG TQKAHTIPSA YWKVIFINNS 200
    PAVNHYAAFL FDQNTPKGAD FCQFRVTVDE IEKRTGLIIW AGLPDDVQAS 250
    LKSKPGVLPE LMGCKN 266
    Length:266
    Mass (Da):28,945
    Last modified:February 1, 1996 - v2
    Checksum:iA0FF0C1430677B9E
    GO

    Mass spectrometryi

    Molecular mass is 26708.2 Da from positions 22 - 266. Determined by ESI. Isoform Sm2.1 Publication
    Molecular mass is 26591.8 Da from positions 23 - 266. Determined by ESI. Isoform Sm3.1 Publication
    Molecular mass is 26376.4 Da from positions 25 - 266. Determined by ESI. Isoform Sm1.1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M19495 Genomic DNA. Translation: AAA26560.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M19495 Genomic DNA. Translation: AAA26560.1 .

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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 [» ]
    4E3Y X-ray 0.95 A/B 22-266 [» ]
    ProteinModelPortali P13717.
    SMRi P13717. Positions 26-266.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi P13717.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei P13717.

    Family and domain databases

    Gene3Di 3.40.570.10. 1 hit.
    InterProi IPR018524. DNA/RNA_endonuclease_AS.
    IPR001604. DNA/RNA_non-sp_Endonuclease.
    IPR020821. Extracellular_endonuc_su_A.
    [Graphical view ]
    Pfami PF01223. Endonuclease_NS. 1 hit.
    [Graphical view ]
    SMARTi SM00892. Endonuclease_NS. 1 hit.
    SM00477. NUC. 1 hit.
    [Graphical view ]
    PROSITEi PS01070. NUCLEASE_NON_SPEC. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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.

    Entry informationi

    Entry nameiNUCA_SERMA
    AccessioniPrimary (citable) accession number: P13717
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 1, 1990
    Last sequence update: February 1, 1996
    Last modified: October 1, 2014
    This is version 96 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    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.

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3