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Protein

Nuclease

Gene

nucA

Organism
Serratia marcescens
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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

Mg2+Note: Binds 1 Mg2+ ion.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei110 – 1101Proton acceptorPROSITE-ProRule annotation1 Publication
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
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BRENDAi3.1.30.2. 5690.

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
Complete GO annotation...

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 – 324Combined sources
Beta strandi39 – 424Combined sources
Beta strandi50 – 534Combined sources
Turni55 – 573Combined sources
Beta strandi58 – 6710Combined sources
Helixi88 – 903Combined sources
Helixi94 – 974Combined sources
Helixi100 – 1045Combined sources
Beta strandi106 – 1127Combined sources
Helixi114 – 1174Combined sources
Helixi123 – 1275Combined sources
Helixi129 – 1313Combined sources
Beta strandi132 – 1365Combined sources
Helixi137 – 1404Combined sources
Helixi143 – 15311Combined sources
Helixi154 – 1563Combined sources
Beta strandi163 – 1708Combined sources
Beta strandi189 – 1979Combined sources
Turni201 – 2033Combined sources
Beta strandi206 – 2127Combined sources
Helixi221 – 2244Combined sources
Helixi228 – 2358Combined sources
Beta strandi238 – 2403Combined sources
Helixi245 – 2517Combined sources
Helixi258 – 2614Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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[»]
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

        10         20         30         40         50
MRFNNKMLAL AALLFAAQAS ADTLESIDNC AVGCPTGGSS NVSIVRHAYT
60 70 80 90 100
LNNNSTTKFA NWVAYHITKD TPASGKTRNW KTDPALNPAD TLAPADYTGA
110 120 130 140 150
NAALKVDRGH QAPLASLAGV SDWESLNYLS NITPQKSDLN QGAWARLEDQ
160 170 180 190 200
ERKLIDRADI SSVYTVTGPL YERDMGKLPG TQKAHTIPSA YWKVIFINNS
210 220 230 240 250
PAVNHYAAFL FDQNTPKGAD FCQFRVTVDE IEKRTGLIIW AGLPDDVQAS
260
LKSKPGVLPE LMGCKN
Length:266
Mass (Da):28,945
Last modified:January 31, 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:
EMBLi
GenBanki
DDBJi
Links Updated
M19495 Genomic DNA. Translation: AAA26560.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M19495 Genomic DNA. Translation: AAA26560.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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[»]
SMRiP13717. Positions 26-266.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiP13717.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi3.1.30.2. 5690.

Miscellaneous databases

EvolutionaryTraceiP13717.

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]
ProtoNetiSearch...

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(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: W225.
  2. Benedick M.J.
    Submitted (SEP-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(1988) [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(1992) [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(1993) [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(1993) [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(1995) [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(1997) [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(1993) [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(1996) [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(1999) [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: December 31, 1989
Last sequence update: January 31, 1996
Last modified: March 31, 2015
This is version 100 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.