NUCA_SERMA
ID NUCA_SERMA Reviewed; 266 AA.
AC P13717;
DT 01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1996, sequence version 2.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Nuclease;
DE EC=3.1.30.2;
DE AltName: Full=Endonuclease;
DE Contains:
DE RecName: Full=Nuclease isoform Sm2;
DE Contains:
DE RecName: Full=Nuclease isoform Sm3;
DE Contains:
DE RecName: Full=Nuclease isoform Sm1;
DE Flags: Precursor;
GN Name=nucA; Synonyms=nuc;
OS Serratia marcescens.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Serratia.
OX NCBI_TaxID=615;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=W225;
RX PubMed=3319779; DOI=10.1016/0378-1119(87)90121-1;
RA Ball T.K., Saurugger P.N., Benedick M.J.;
RT "The extracellular nuclease gene of Serratia marcescens and its secretion
RT from Escherichia coli.";
RL Gene 57:183-192(1987).
RN [2]
RP SEQUENCE REVISION TO 7-11.
RA Benedick M.J.;
RL Submitted (OCT-1989) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP PARTIAL PROTEIN SEQUENCE, AND DISULFIDE BONDS.
RX PubMed=2665765; DOI=10.1007/bf02910469;
RA Biedermann K., Jepsen P.K., Riise E., Svendsen I.;
RT "Purification and characterization of a Serratia marcescens nuclease
RT produced by Escherichia coli.";
RL Carlsberg Res. Commun. 54:17-27(1989).
RN [4]
RP IDENTIFICATION OF ISOFORMS SM1; SM2 AND SM3, MASS SPECTROMETRY, AND
RP DISULFIDE BONDS.
RC STRAIN=B10M1;
RX PubMed=8373817; DOI=10.1016/0167-4838(93)90057-x;
RA Pedersen J., Filimonova M.N., Roepstorff P., Biedermann K.;
RT "Characterization of Serratia marcescens nuclease isoforms by plasma
RT desorption mass spectrometry.";
RL Biochim. Biophys. Acta 1202:13-21(1993).
RN [5]
RP ACTIVE SITE.
RX PubMed=8078761; DOI=10.1093/nar/22.16.3280;
RA Friedhoff P., Gimadutdinow O., Pingoud A.;
RT "Identification of catalytically relevant amino acids of the extracellular
RT Serratia marcescens endonuclease by alignment-guided mutagenesis.";
RL Nucleic Acids Res. 22:3280-3287(1994).
RN [6]
RP BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=7804150;
RA Filimonova M.N., Krause K.L., Benedik M.J.;
RT "Kinetic studies of the Serratia marcescens extracellular nuclease
RT isoforms.";
RL Biochem. Mol. Biol. Int. 33:1229-1236(1994).
RN [7]
RP MUTAGENESIS OF ARG-78; ARG-108; HIS-110; ASN-140 AND GLU-148.
RX PubMed=8758988; DOI=10.1093/nar/24.14.2632;
RA Friedhoff P., Kolmes B., Gimadutdinow O., Wende W., Krause K.L.,
RA Pingoud A.;
RT "Analysis of the mechanism of the Serratia nuclease using site-directed
RT mutagenesis.";
RL Nucleic Acids Res. 24:2632-2639(1996).
RN [8]
RP REVIEW.
RX PubMed=9711834; DOI=10.1111/j.1574-6968.1998.tb13120.x;
RA Benedik M.J., Strych U.;
RT "Serratia marcescens and its extracellular nuclease.";
RL FEMS Microbiol. Lett. 165:1-13(1998).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH MAGNESIUM IONS, AND
RP SUBUNIT.
RX PubMed=7664065; DOI=10.1038/nsb0794-461;
RA Miller M.D., Tanner J., Alpaugh M., Benedik M.J., Krause K.L.;
RT "2.1-A structure of Serratia endonuclease suggests a mechanism for binding
RT to double-stranded DNA.";
RL Nat. Struct. Biol. 1:461-468(1994).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
RX PubMed=9257723; DOI=10.1016/s0014-5793(97)00512-7;
RA Lunin V.Y., Levdikov V.M., Shlyapnikov S.V., Blagova E.V., Lunin V.V.,
RA Wilson K.S., Mikhailov A.M.;
RT "Three-dimensional structure of Serratia marcescens nuclease at 1.7-A
RT resolution and mechanism of its action.";
RL FEBS Lett. 412:217-222(1997).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.1 ANGSTROMS) OF 22-266 IN COMPLEX WITH MAGNESIUM
RP IONS.
RX PubMed=10771425; DOI=10.1107/s090744490000322x;
RA Shlyapnikov S.V., Lunin V.V., Perbandt M., Polyakov K.M., Lunin V.Y.,
RA Levdikov V.M., Betzel C., Mikhailov A.M.;
RT "Atomic structure of the Serratia marcescens endonuclease at 1.1 A
RT resolution and the enzyme reaction mechanism.";
RL Acta Crystallogr. D 56:567-572(2000).
CC -!- FUNCTION: Catalyzes the hydrolysis of both DNA and RNA, double- or
CC single-stranded, at the 3'position of the phosphodiester bond to
CC produce 5'-phosphorylated mono-, di-, tri- and tetranucleotides. DNA is
CC a slightly better substrate than RNA.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-
CC phosphooligonucleotide end-products.; EC=3.1.30.2;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU10047};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Note=Binds 1 Mg(2+) ion.;
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10771425,
CC ECO:0000269|PubMed:7664065}.
CC -!- SUBCELLULAR LOCATION: Secreted.
CC -!- MASS SPECTROMETRY: [Nuclease isoform Sm2]: Mass=26708.2;
CC Method=Electrospray; Note=Isoform Sm2.;
CC Evidence={ECO:0000269|PubMed:8373817};
CC -!- MASS SPECTROMETRY: [Nuclease isoform Sm3]: Mass=26591.8;
CC Method=Electrospray; Note=Isoform Sm3.;
CC Evidence={ECO:0000269|PubMed:8373817};
CC -!- MASS SPECTROMETRY: [Nuclease isoform Sm1]: Mass=26376.4;
CC Method=Electrospray; Note=Isoform Sm1.;
CC Evidence={ECO:0000269|PubMed:8373817};
CC -!- MISCELLANEOUS: The active site contains 1 hydrated magnesium ion that
CC has only 1 direct interaction with the protein; all other interactions
CC are via water molecules.
CC -!- SIMILARITY: Belongs to the DNA/RNA non-specific endonuclease family.
CC {ECO:0000305}.
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DR EMBL; M19495; AAA26560.1; -; Genomic_DNA.
DR RefSeq; WP_015377376.1; NZ_WVHX01000034.1.
DR PDB; 1G8T; X-ray; 1.10 A; A/B=22-266.
DR PDB; 1QAE; X-ray; 2.05 A; A/B=22-266.
DR PDB; 1QL0; X-ray; 1.10 A; A/B=26-266.
DR PDB; 1SMN; X-ray; 2.04 A; A/B=22-266.
DR PDB; 4E3Y; X-ray; 0.95 A; A/B=22-266.
DR PDBsum; 1G8T; -.
DR PDBsum; 1QAE; -.
DR PDBsum; 1QL0; -.
DR PDBsum; 1SMN; -.
DR PDBsum; 4E3Y; -.
DR AlphaFoldDB; P13717; -.
DR SMR; P13717; -.
DR STRING; 273526.SMDB11_1061; -.
DR PRIDE; P13717; -.
DR GeneID; 66715254; -.
DR OrthoDB; 1438016at2; -.
DR BRENDA; 3.1.30.2; 5690.
DR EvolutionaryTrace; P13717; -.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR Gene3D; 3.40.570.10; -; 1.
DR InterPro; IPR018524; DNA/RNA_endonuclease_AS.
DR InterPro; IPR001604; DNA/RNA_non-sp_Endonuclease.
DR InterPro; IPR044929; DNA/RNA_non-sp_Endonuclease_sf.
DR InterPro; IPR020821; Extracellular_endonuc_su_A.
DR InterPro; IPR044925; His-Me_finger_sf.
DR InterPro; IPR040255; Non-specific_endonuclease.
DR PANTHER; PTHR13966; PTHR13966; 1.
DR Pfam; PF01223; Endonuclease_NS; 1.
DR SMART; SM00892; Endonuclease_NS; 1.
DR SMART; SM00477; NUC; 1.
DR SUPFAM; SSF54060; SSF54060; 1.
DR PROSITE; PS01070; NUCLEASE_NON_SPEC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Disulfide bond; Endonuclease;
KW Hydrolase; Magnesium; Metal-binding; Nuclease; Secreted; Signal.
FT SIGNAL 1..21
FT CHAIN 22..266
FT /note="Nuclease isoform Sm2"
FT /id="PRO_0000019914"
FT CHAIN 23..266
FT /note="Nuclease isoform Sm3"
FT /id="PRO_0000019915"
FT CHAIN 25..266
FT /note="Nuclease isoform Sm1"
FT /id="PRO_0000019916"
FT ACT_SITE 110
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10047,
FT ECO:0000269|PubMed:8078761"
FT BINDING 140
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT DISULFID 30..34
FT DISULFID 222..264
FT MUTAGEN 78
FT /note="R->A: Reduced activity 1000-fold."
FT /evidence="ECO:0000269|PubMed:8758988"
FT MUTAGEN 78
FT /note="R->K: Reduced activity 100-fold."
FT /evidence="ECO:0000269|PubMed:8758988"
FT MUTAGEN 108
FT /note="R->A: Reduced activity 1000-fold."
FT /evidence="ECO:0000269|PubMed:8758988"
FT MUTAGEN 108
FT /note="R->K: Reduced activity 50-fold."
FT /evidence="ECO:0000269|PubMed:8758988"
FT MUTAGEN 110
FT /note="H->A,D,E,K,Q: Reduced activity 100000-fold."
FT /evidence="ECO:0000269|PubMed:8758988"
FT MUTAGEN 110
FT /note="H->N: Reduced activity 1000-fold."
FT /evidence="ECO:0000269|PubMed:8758988"
FT MUTAGEN 140
FT /note="N->A,D,H: Reduced activity over 10000-fold."
FT /evidence="ECO:0000269|PubMed:8758988"
FT MUTAGEN 140
FT /note="N->Q: Reduced activity 1000-fold."
FT /evidence="ECO:0000269|PubMed:8758988"
FT MUTAGEN 148
FT /note="E->A,D,Q: Reduced activity over 800-fold."
FT /evidence="ECO:0000269|PubMed:8758988"
FT STRAND 29..32
FT /evidence="ECO:0007829|PDB:4E3Y"
FT STRAND 39..42
FT /evidence="ECO:0007829|PDB:1QAE"
FT STRAND 50..53
FT /evidence="ECO:0007829|PDB:4E3Y"
FT TURN 55..57
FT /evidence="ECO:0007829|PDB:4E3Y"
FT STRAND 58..67
FT /evidence="ECO:0007829|PDB:4E3Y"
FT HELIX 88..90
FT /evidence="ECO:0007829|PDB:4E3Y"
FT HELIX 94..97
FT /evidence="ECO:0007829|PDB:4E3Y"
FT HELIX 100..104
FT /evidence="ECO:0007829|PDB:4E3Y"
FT STRAND 106..112
FT /evidence="ECO:0007829|PDB:4E3Y"
FT HELIX 114..117
FT /evidence="ECO:0007829|PDB:4E3Y"
FT HELIX 123..127
FT /evidence="ECO:0007829|PDB:4E3Y"
FT HELIX 129..131
FT /evidence="ECO:0007829|PDB:4E3Y"
FT STRAND 132..136
FT /evidence="ECO:0007829|PDB:4E3Y"
FT HELIX 137..140
FT /evidence="ECO:0007829|PDB:4E3Y"
FT HELIX 143..153
FT /evidence="ECO:0007829|PDB:4E3Y"
FT HELIX 154..156
FT /evidence="ECO:0007829|PDB:4E3Y"
FT STRAND 163..170
FT /evidence="ECO:0007829|PDB:4E3Y"
FT STRAND 189..197
FT /evidence="ECO:0007829|PDB:4E3Y"
FT TURN 201..203
FT /evidence="ECO:0007829|PDB:4E3Y"
FT STRAND 206..212
FT /evidence="ECO:0007829|PDB:4E3Y"
FT HELIX 221..224
FT /evidence="ECO:0007829|PDB:4E3Y"
FT HELIX 228..235
FT /evidence="ECO:0007829|PDB:4E3Y"
FT STRAND 238..240
FT /evidence="ECO:0007829|PDB:4E3Y"
FT HELIX 245..251
FT /evidence="ECO:0007829|PDB:4E3Y"
FT HELIX 258..261
FT /evidence="ECO:0007829|PDB:4E3Y"
SQ SEQUENCE 266 AA; 28945 MW; A0FF0C1430677B9E CRC64;
MRFNNKMLAL AALLFAAQAS ADTLESIDNC AVGCPTGGSS NVSIVRHAYT LNNNSTTKFA
NWVAYHITKD TPASGKTRNW KTDPALNPAD TLAPADYTGA NAALKVDRGH QAPLASLAGV
SDWESLNYLS NITPQKSDLN QGAWARLEDQ ERKLIDRADI SSVYTVTGPL YERDMGKLPG
TQKAHTIPSA YWKVIFINNS PAVNHYAAFL FDQNTPKGAD FCQFRVTVDE IEKRTGLIIW
AGLPDDVQAS LKSKPGVLPE LMGCKN
