ID YHCR_BACSU Reviewed; 1217 AA.
AC P54602;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 27-MAR-2024, entry version 160.
DE RecName: Full=Endonuclease YhcR;
DE EC=3.1.31.- {ECO:0000269|PubMed:15292138};
DE Flags: Precursor;
GN Name=yhcR; OrderedLocusNames=BSU09190;
OS Bacillus subtilis (strain 168).
OC Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=8969498; DOI=10.1099/13500872-142-11-3021;
RA Noback M.A., Terpstra P., Holsappel S., Venema G., Bron S.;
RT "A 22 kb DNA sequence in the cspB-glpPFKD region at 75 degrees on the
RT Bacillus subtilis chromosome.";
RL Microbiology 142:3021-3026(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP FUNCTION, COFACTOR, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP SUBCELLULAR LOCATION.
RX PubMed=15292138; DOI=10.1128/jb.186.16.5376-5383.2004;
RA Oussenko I.A., Sanchez R., Bechhofer D.H.;
RT "Bacillus subtilis YhcR, a high-molecular-weight, nonspecific endonuclease
RT with a unique domain structure.";
RL J. Bacteriol. 186:5376-5383(2004).
RN [4]
RP SUBCELLULAR LOCATION, AND PROCESSING BY SORTASE D.
RX PubMed=21906378; DOI=10.1186/2191-0855-1-22;
RA Nguyen H.D., Phan T.T., Schumann W.;
RT "Analysis and application of Bacillus subtilis sortases to anchor
RT recombinant proteins on the cell wall.";
RL AMB Express 1:22-22(2011).
RN [5]
RP SUBCELLULAR LOCATION, AND PROCESSING BY SORTASE D.
RX PubMed=22020651; DOI=10.1128/jb.05711-11;
RA Liew P.X., Wang C.L., Wong S.L.;
RT "Functional characterization and localization of a Bacillus subtilis
RT sortase and its substrate and use of this sortase system to covalently
RT anchor a heterologous protein to the B. subtilis cell wall for surface
RT display.";
RL J. Bacteriol. 194:161-175(2012).
CC -!- FUNCTION: Sugar-nonspecific endonuclease that yields nucleotide 3'-
CC monophosphate products. No 5'-nucleotidase activity was detected, using
CC 5'-AMP as the substrate, in the presence of diverse divalent metals and
CC with various pH values. {ECO:0000269|PubMed:15292138}.
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000269|PubMed:15292138};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:15292138};
CC -!- ACTIVITY REGULATION: Requires a minimum of 0.1 mM of calcium for a
CC significant activity. Maximal activity was observed with concentrations
CC of calcium between 1 to 5 mM. Is 10-fold less active with the
CC corresponding concentrations of manganese. Inhibited by NaCl at
CC concentrations of 100 mM and higher. {ECO:0000269|PubMed:15292138}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 9.0. {ECO:0000269|PubMed:15292138};
CC -!- SUBCELLULAR LOCATION: Secreted, cell wall {ECO:0000269|PubMed:15292138,
CC ECO:0000269|PubMed:21906378, ECO:0000269|PubMed:22020651};
CC Peptidoglycan-anchor {ECO:0000255|PROSITE-ProRule:PRU00477}.
CC Note=Anchored to the cell wall by sortase SrtD.
CC {ECO:0000269|PubMed:21906378, ECO:0000269|PubMed:22020651}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the 5'-nucleotidase
CC family. {ECO:0000305}.
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DR EMBL; X96983; CAA65702.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB12747.1; -; Genomic_DNA.
DR PIR; F69823; F69823.
DR RefSeq; NP_388800.1; NC_000964.3.
DR RefSeq; WP_010886455.1; NZ_JNCM01000035.1.
DR AlphaFoldDB; P54602; -.
DR SMR; P54602; -.
DR IntAct; P54602; 3.
DR STRING; 224308.BSU09190; -.
DR PaxDb; 224308-BSU09190; -.
DR EnsemblBacteria; CAB12747; CAB12747; BSU_09190.
DR GeneID; 936241; -.
DR KEGG; bsu:BSU09190; -.
DR PATRIC; fig|224308.43.peg.960; -.
DR eggNOG; COG0737; Bacteria.
DR eggNOG; COG1525; Bacteria.
DR eggNOG; COG4085; Bacteria.
DR InParanoid; P54602; -.
DR OrthoDB; 9775118at2; -.
DR BioCyc; BSUB:BSU09190-MONOMER; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-KW.
DR GO; GO:0030288; C:outer membrane-bounded periplasmic space; IBA:GO_Central.
DR GO; GO:0008253; F:5'-nucleotidase activity; IBA:GO_Central.
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 GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0008768; F:UDP-sugar diphosphatase activity; IBA:GO_Central.
DR GO; GO:0009166; P:nucleotide catabolic process; IEA:InterPro.
DR CDD; cd07412; MPP_YhcR_N; 1.
DR CDD; cd00175; SNc; 1.
DR CDD; cd04486; YhcR_OBF_like; 2.
DR Gene3D; 2.40.50.90; -; 1.
DR Gene3D; 3.60.21.10; -; 1.
DR Gene3D; 3.90.780.10; 5'-Nucleotidase, C-terminal domain; 1.
DR InterPro; IPR008334; 5'-Nucleotdase_C.
DR InterPro; IPR036907; 5'-Nucleotdase_C_sf.
DR InterPro; IPR006146; 5'-Nucleotdase_CS.
DR InterPro; IPR006179; 5_nucleotidase/apyrase.
DR InterPro; IPR004843; Calcineurin-like_PHP_ApaH.
DR InterPro; IPR019931; LPXTG_anchor.
DR InterPro; IPR029052; Metallo-depent_PP-like.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR004365; NA-bd_OB_tRNA.
DR InterPro; IPR035437; SNase_OB-fold_sf.
DR InterPro; IPR016071; Staphylococal_nuclease_OB-fold.
DR InterPro; IPR041831; YhcR_MPP.
DR InterPro; IPR045939; YhcR_N.
DR NCBIfam; TIGR01167; LPXTG_anchor; 1.
DR PANTHER; PTHR11575:SF48; 5' NUCLEOTIDASE, ECTO-LIKE; 1.
DR PANTHER; PTHR11575; 5'-NUCLEOTIDASE-RELATED; 1.
DR Pfam; PF02872; 5_nucleotid_C; 1.
DR Pfam; PF19886; DUF6359; 1.
DR Pfam; PF00746; Gram_pos_anchor; 1.
DR Pfam; PF00149; Metallophos; 1.
DR Pfam; PF00565; SNase; 1.
DR Pfam; PF01336; tRNA_anti-codon; 1.
DR PRINTS; PR01607; APYRASEFAMLY.
DR SMART; SM00318; SNc; 1.
DR SUPFAM; SSF55816; 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain; 1.
DR SUPFAM; SSF56300; Metallo-dependent phosphatases; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR SUPFAM; SSF50199; Staphylococcal nuclease; 1.
DR PROSITE; PS00786; 5_NUCLEOTIDASE_2; 1.
DR PROSITE; PS50847; GRAM_POS_ANCHORING; 1.
DR PROSITE; PS50830; TNASE_3; 1.
PE 1: Evidence at protein level;
KW Calcium; Cell wall; Endonuclease; Hydrolase; Manganese; Metal-binding;
KW Nuclease; Nucleotide-binding; Peptidoglycan-anchor; Reference proteome;
KW Secreted; Signal.
FT SIGNAL 1..46
FT /evidence="ECO:0000255"
FT CHAIN 47..1185
FT /note="Endonuclease YhcR"
FT /id="PRO_0000000040"
FT PROPEP 1186..1217
FT /note="Removed by sortase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00477"
FT /id="PRO_0000445194"
FT DOMAIN 376..517
FT /note="TNase-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00272"
FT REGION 590..828
FT /note="Phosphoesterase"
FT REGION 829..1085
FT /note="5'-nucleotidase"
FT REGION 1087..1142
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 1182..1186
FT /note="LPXTG sorting signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00477"
FT COMPBIAS 1092..1110
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1111..1126
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 404
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00272"
FT ACT_SITE 412
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00272"
FT ACT_SITE 460
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00272"
FT BINDING 597
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 599
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 647
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 647
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 680
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 792
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 824
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 965
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 1035..1042
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 681
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250"
FT SITE 684
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250"
FT MOD_RES 1185
FT /note="Pentaglycyl murein peptidoglycan amidated threonine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00477"
SQ SEQUENCE 1217 AA; 132686 MW; 7973160CC898DC0B CRC64;
MLSVEMISRQ NRCHYVYKGG NMMRRILHIV LITALMFLNV MYTFEAVKAA EPQQPISIEK
AIQQKEGQAL VEGYAVGQAV SPQHYKLTSP FSNDYNVALA DRKNKTSPEH ILPVQIPSAF
RSQFGLQTNP LLLGKKITVQ GKLENYFNTT GLKNVQSMNV TDDTKTPPAE QQVTINEARG
RLNEEVTIKG IITADQNAIG GGKLSTFLQD ETGGINIYSP SPEQFPELKE GMDVTVTGKI
TSYQGLKEIV PNSSGIKINQ SNQSLPAPKH LTINELINGS LGDQYEGRLV KLTAFVSSIP
SSPAGGGYNV TMIDDDHHAM TLRVMNETGV INELDEGKWY EFTGVLSRYQ TFQLLPRKSA
DLKLLEEQPA PPSAEGEYEG IVDRVVDGDT IHLKSPVLGT TKIRFVNVDA PETYHTPKND
ADENQLRFGK KASDYLKTVL SPGDKITVKV GSEAKDSYGR LLGQVITESG SNVNLELVKN
GYAPTYFIWP VDNEEDYQQF QAAVAAAKKD QKGIWNENDP LMEMPFEFRA REQGKGLTRY
VGDSSNKTYV QPADWKKIAV ENRIFFASAS EAESAGYKKR QTAPQEHVPL RILSMNDLHG
KIDQQYELDL DGNGTVDGTF GRMDYAAAYL KEKKAEKKNS LIVHAGDMIG GSSPVSSLLQ
DEPTVELMED IGFDVGTVGN HEFDEGTDEL LRILNGGDHP KGTSGYDGQN FPLVCANCKM
KSTGEPFLPA YDIINVEGVP VAFIGVVTQS AAGMVMPEGI KNIEFTDEAT AVNKAAEELK
KKGVKAIAVL AHMSAEQNGN AITGESADLA NKTDSEIDVI FAAHNHQVVN GEVNGKLIVQ
AFEYGKAIGV VDVEIDKTTK DIVKKSAEIV YVDQSKIEPD VSASAILKKY ETIAEPIISE
VVGEAAVDME GGYSNDGDTP LGNLIADGMR AAMKTDFALM NGGGIREALK KGPITWGDLY
NIQPFGNVLT KLEIKGKDLR EIINAQISPV FGPDYSISGF TYTWDKETGK AVDMKMADGT
EIQPDATYTL TVNNFMATAT GAKYQPIGLL GKNPVTGPED LEATVEYVKS FDEPIAYTKE
GRIKLAEASD IEDPVTEDPI TEEPGDDPGT EDPIKEDPRP GEDLPDIKET PGTAPVHQLP
PSAISRFNEI PINNTKTADT ANSISTLPLQ TETAESGSDH QLPDTSAGYY NFMVIGAAVT
LSGTYLYVRR KRSASRT
//
