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P13717

- NUCA_SERMA

UniProt

P13717 - NUCA_SERMA

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Protein
Nuclease
Gene
nucA, nuc
Organism
Serratia marcescens
Status
Reviewed - 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.

Cofactori

Binds 1 magnesium ion.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei110 – 1101Proton acceptor1 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

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 – 2121
Add
BLAST
Chaini22 – 266245Nuclease isoform Sm2
PRO_0000019914Add
BLAST
Chaini23 – 266244Nuclease isoform Sm3
PRO_0000019915Add
BLAST
Chaini25 – 266242Nuclease isoform Sm1
PRO_0000019916Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi30 ↔ 342 Publications
Disulfide bondi222 ↔ 2642 Publications

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiP13717.

Interactioni

Subunit structurei

Homodimer.1 Publication

Structurei

Secondary structure

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.

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: June 11, 2014
This is version 95 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

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