WAPA_BACSU
ID WAPA_BACSU Reviewed; 2334 AA.
AC Q07833;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 28-JUL-2009, sequence version 2.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=tRNA nuclease WapA;
DE EC=3.1.-.-;
DE AltName: Full=Cell wall-associated polypeptide CWBP200;
DE Short=CWBP200;
DE AltName: Full=RNase WapA;
DE AltName: Full=Toxin WapA;
DE AltName: Full=Wall-associated protein;
DE Flags: Precursor;
GN Name=wapA; OrderedLocusNames=BSU39230; ORFNames=N17G;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=8316082; DOI=10.1111/j.1365-2958.1993.tb01574.x;
RA Foster S.J.;
RT "Molecular analysis of three major wall-associated proteins of Bacillus
RT subtilis 168: evidence for processing of the product of a gene encoding a
RT 258 kDa precursor two-domain ligand-binding protein.";
RL Mol. Microbiol. 8:299-310(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / BGSC1A1;
RX PubMed=7704263; DOI=10.1099/13500872-141-2-337;
RA Yoshida K., Sano H., Seki S., Oda M., Fujimura M., Fujita Y.;
RT "Cloning and sequencing of a 29 kb region of the Bacillus subtilis genome
RT containing the hut and wapA loci.";
RL Microbiology 141:337-343(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / BGSC1A1;
RX PubMed=8969509; DOI=10.1099/13500872-142-11-3113;
RA Yoshida K., Shindo K., Sano H., Seki S., Fujimura M., Yanai N., Miwa Y.,
RA Fujita Y.;
RT "Sequencing of a 65 kb region of the Bacillus subtilis genome containing
RT the lic and cel loci, and creation of a 177 kb contig covering the gnt-
RT sacXY region.";
RL Microbiology 142:3113-3123(1996).
RN [4]
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 [5]
RP SEQUENCE REVISION TO 1312-1313.
RX PubMed=19383706; DOI=10.1099/mic.0.027839-0;
RA Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A.,
RA Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
RT "From a consortium sequence to a unified sequence: the Bacillus subtilis
RT 168 reference genome a decade later.";
RL Microbiology 155:1758-1775(2009).
RN [6]
RP PROTEIN SEQUENCE OF 97-107, AND SUBCELLULAR LOCATION.
RC STRAIN=168;
RX PubMed=10658653; DOI=10.1099/00221287-146-1-65;
RA Hirose I., Sano K., Shioda I., Kumano M., Nakamura K., Yamane K.;
RT "Proteome analysis of Bacillus subtilis extracellular proteins: a two-
RT dimensional protein electrophoretic study.";
RL Microbiology 146:65-75(2000).
RN [7]
RP ACTIVITY REGULATION, SUBCELLULAR LOCATION, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC STRAIN=168;
RX PubMed=11987133;
RX DOI=10.1002/1615-9861(200205)2:5<591::aid-prot591>3.0.co;2-8;
RA Antelmann H., Yamamoto H., Sekiguchi J., Hecker M.;
RT "Stabilization of cell wall proteins in Bacillus subtilis: a proteomic
RT approach.";
RL Proteomics 2:591-602(2002).
RN [8]
RP FUNCTION AS A TRNA NUCLEASE, FUNCTION AS A TOXIN, EXPRESSION IN E.COLI, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=168;
RX PubMed=23572593; DOI=10.1073/pnas.1300627110;
RA Koskiniemi S., Lamoureux J.G., Nikolakakis K.C., t'Kint de Roodenbeke C.,
RA Kaplan M.D., Low D.A., Hayes C.S.;
RT "Rhs proteins from diverse bacteria mediate intercellular competition.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:7032-7037(2013).
RN [9]
RP INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=34280190; DOI=10.1371/journal.pgen.1009682;
RA Kobayashi K.;
RT "Diverse LXG toxin and antitoxin systems specifically mediate intraspecies
RT competition in Bacillus subtilis biofilms.";
RL PLoS Genet. 17:e1009682-e1009682(2021).
CC -!- FUNCTION: Toxic component of a toxin-immunity protein module, which
CC functions as a cellular contact-dependent growth inhibition (CDI)
CC system. A site-specific general tRNA nuclease, the C-terminus (residues
CC 2201-2334) removes 2 or 4 nucleotides from the 3' end of at least 4
CC tRNAs (upon expression in E.coli), possibly endonucleolytically. The
CC nuclease activity is neutralized by expression of the cognate immunity
CC protein WapI from the same strain, but not its homolog from 2 other
CC B.subtilis strains. The C-terminus cannot be expressed on its own in
CC E.coli, however it can be cloned in the presence of its cognate
CC immunity protein gene. Cell contact is necessary for growth inhibition
CC (PubMed:23572593). Unlike the LXG toxin-immunity modules, WapAI
CC mediates competition under shaking culture conditions
CC (PubMed:34280190). {ECO:0000269|PubMed:23572593,
CC ECO:0000269|PubMed:34280190}.
CC -!- ACTIVITY REGULATION: Detected in exponentially growing cells as many
CC processing products, protein disappears upon entry into stationary
CC phase with the concomitant appearance of smaller products. The large
CC products persist in the absence of the extracellular serine protease
CC Epr (PubMed:11987133). {ECO:0000269|PubMed:11987133}.
CC -!- SUBCELLULAR LOCATION: Secreted, cell wall
CC {ECO:0000269|PubMed:11987133}. Secreted {ECO:0000269|PubMed:10658653}.
CC Note=Probably exported by a SecA-dependent pathway.
CC {ECO:0000269|PubMed:10658653}.
CC -!- INDUCTION: Constitutively and highly expressed on solid and in liquid
CC medium, with or without biofilm formation, by 12 hours of culture.
CC Repressed by DegU. {ECO:0000269|PubMed:34280190}.
CC -!- DOMAIN: Has two ligand-binding domains; the N-terminus has three 101 AA
CC repeats which are responsible for cell wall binding; the C-terminus
CC consists of two blocks of residues with a conserved motif repeated 31
CC times.
CC -!- PTM: Identified in the extracellular proteome as many processing
CC products ranging from over 85 kDa to about 30 kDa. One of these
CC probably starts on Ser-1726. Two forms are known as CWBP62 and CWBP105
CC (PubMed:11987133). {ECO:0000269|PubMed:11987133}.
CC -!- DISRUPTION PHENOTYPE: A double wapA-wapI deletion strain is growth
CC inhibited when cocultured with wild-type cells. When wapI is
CC reintroduced it restores growth in a cognate toxin-dependent fashion
CC (PubMed:23572593). Growth inhibition by wild-type cells is strongest on
CC LB medium and less effective on media that promote biofilm formation
CC (MSgg and 2xSGG) (PubMed:34280190). {ECO:0000269|PubMed:23572593,
CC ECO:0000269|PubMed:34280190}.
CC -!- SIMILARITY: Belongs to the RHS/WapA nuclease family. {ECO:0000305}.
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DR EMBL; L05634; AAA22883.1; -; Genomic_DNA.
DR EMBL; D31856; BAA06656.1; -; Genomic_DNA.
DR EMBL; D29985; BAA06260.1; -; Genomic_DNA.
DR EMBL; D83026; BAA11683.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB15959.2; -; Genomic_DNA.
DR PIR; S32920; S32920.
DR RefSeq; NP_391802.2; NC_000964.3.
DR RefSeq; WP_003243665.1; NZ_JNCM01000034.1.
DR AlphaFoldDB; Q07833; -.
DR SMR; Q07833; -.
DR IntAct; Q07833; 1.
DR STRING; 224308.BSU39230; -.
DR jPOST; Q07833; -.
DR PaxDb; Q07833; -.
DR PRIDE; Q07833; -.
DR EnsemblBacteria; CAB15959; CAB15959; BSU_39230.
DR GeneID; 937525; -.
DR KEGG; bsu:BSU39230; -.
DR PATRIC; fig|224308.179.peg.4247; -.
DR eggNOG; COG3209; Bacteria.
DR InParanoid; Q07833; -.
DR OMA; GKKIWPT; -.
DR BioCyc; BSUB:BSU39230-MON; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-KW.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0090729; F:toxin activity; IEA:UniProtKB-KW.
DR GO; GO:0004549; F:tRNA-specific ribonuclease activity; IDA:UniProtKB.
DR GO; GO:0016078; P:tRNA catabolic process; IDA:UniProtKB.
DR Gene3D; 2.60.40.10; -; 1.
DR InterPro; IPR045351; DUF6531.
DR InterPro; IPR008979; Galactose-bd-like_sf.
DR InterPro; IPR013783; Ig-like_fold.
DR InterPro; IPR022385; Rhs_assc_core.
DR InterPro; IPR031325; RHS_repeat.
DR InterPro; IPR006530; YD.
DR Pfam; PF20148; DUF6531; 1.
DR Pfam; PF05593; RHS_repeat; 4.
DR SUPFAM; SSF49785; SSF49785; 1.
DR TIGRFAMs; TIGR03696; Rhs_assc_core; 1.
DR TIGRFAMs; TIGR01643; YD_repeat_2x; 5.
PE 1: Evidence at protein level;
KW Cell wall; Direct protein sequencing; Endonuclease; Hydrolase; Nuclease;
KW Reference proteome; Repeat; Secreted; Signal; Toxin; Virulence.
FT SIGNAL 1..28
FT /note="Or 32"
FT /evidence="ECO:0000255"
FT CHAIN 29..2334
FT /note="tRNA nuclease WapA"
FT /id="PRO_0000022689"
FT REPEAT 504..605
FT /note="1-1"
FT REPEAT 636..736
FT /note="1-2"
FT REPEAT 769..869
FT /note="1-3"
FT REPEAT 1021..1040
FT /note="2-1"
FT REPEAT 1032..1065
FT /note="YD 1"
FT REPEAT 1042..1061
FT /note="2-2"
FT REPEAT 1063..1082
FT /note="2-3"
FT REPEAT 1075..1103
FT /note="YD 2"
FT REPEAT 1083..1102
FT /note="2-4"
FT REPEAT 1109..1128
FT /note="2-5"
FT REPEAT 1129..1148
FT /note="2-6"
FT REPEAT 1150..1169
FT /note="2-7"
FT REPEAT 1174..1193
FT /note="2-8"
FT REPEAT 1199..1218
FT /note="2-9"
FT REPEAT 1219..1238
FT /note="2-10"
FT REPEAT 1636..1671
FT /note="YD 3"
FT REPEAT 1646..1665
FT /note="2-11"
FT REPEAT 1667..1686
FT /note="2-12"
FT REPEAT 1690..1709
FT /note="2-13"
FT REPEAT 1711..1730
FT /note="2-14"
FT REPEAT 1732..1751
FT /note="2-15"
FT REPEAT 1753..1772
FT /note="2-16"
FT REPEAT 1795..1814
FT /note="2-17"
FT REPEAT 1820..1839
FT /note="2-18"
FT REPEAT 1840..1859
FT /note="2-19"
FT REPEAT 1861..1880
FT /note="2-20"
FT REPEAT 1887..1906
FT /note="2-21"
FT REPEAT 1898..1935
FT /note="YD 4"
FT REPEAT 1908..1927
FT /note="2-22"
FT REPEAT 1929..1948
FT /note="2-23"
FT REPEAT 1969..1982
FT /note="2-24; approximate"
FT REPEAT 1983..2002
FT /note="2-25"
FT REPEAT 2008..2027
FT /note="2-26"
FT REPEAT 2028..2047
FT /note="2-27"
FT REPEAT 2051..2070
FT /note="2-28"
FT REPEAT 2071..2090
FT /note="2-29"
FT REPEAT 2082..2113
FT /note="YD 5"
FT REPEAT 2093..2112
FT /note="2-30"
FT REPEAT 2120..2139
FT /note="2-31"
FT REGION 36..59
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 504..869
FT /note="3 X 101 AA approximate tandem repeats"
FT REGION 1021..2139
FT /note="31 X 21 AA approximate tandem repeats of X(4)-G-
FT X(4)-[YF]-X-D-X(2)-G-X(4)"
FT REGION 2312..2334
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 2317..2334
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 1312..1313
FT /note="SG -> RR (in Ref. 1; AAA22883, 2; BAA06656 and 3;
FT BAA06260)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 2334 AA; 258162 MW; DAE0897CD279AEB6 CRC64;
MKKRKRRNFK RFIAAFLVLA LMISLVPADV LAKSTEEENG NRIAADDPEE TLQKEQTEEA
VPFDPKDINK EGEITSERTE NTKLYYEGDG VYKQEVYLDP IHTKETPDAD WEDISPELKE
STSKQVETEN AILNSDFQKQ MKNGLYATFE HNDHKVTYSL AEAKGPNKTS LTPKDTSADY
KTDSNEIVYP DVFPNIDLQT FTFNENIKED LVLHQYNGYN TFTFQLKTDL QAKEQEDGSI
DFSDEKGKVV FSVPKPFMTD SKLDELSGEV ERSDKVSYKL EKNEEGYLLH LTADENWLKD
PERVYPVSID PSTSLSVSSD TFVMSAYPTT NYSASSQKWD ANLKAYVLKT GYYDKTTGTN
YAFMKFNNLK PIQNMTVTKA TLKTYVAHSY YGTKATGLWL DTVNSNYDNA KVTWNTKPAS
KNIGKADVHK GQWASYDVTA AVKSWNSGGA NYGFKLHTNG NGKEYWKKLI SSANSANKPY
IEVTYTIPKG NTPTIKAYHN GDSTGYFDIS WKKVEGAKGY KVWIYNGKEY QAISAGNVTS
WSTKGKKIWP TSAEIASKRY KLHLDGKDGA ELALDPSPVY KNSGGSYATS KNYWIGVSAI
FDQGEGAMSA PAKPVIPNVG KAQAPSAKGY NNGNATGYFD LSWKAVSGAT GYKVQVFNGK
GFETLDLGNQ TSWTTKGKKI WPTSAEIKAG KYALHLKDGS GAELPINPGP TYKNAGGDGA
KRNYSFKIIA YNKDGEAIAS PAATPALPDI ARPKNVTGYL YTNTKSSQTG YVNLIWEKVQ
NAKGYKVNIY NGKEYQSFDV GDADHWTTQN KNIWPTSEEI KAGSYKLHTD GKGGELALDP
SPVYNNANGN YKGKKNYSFT LVAYDANGET IPTAPFNPTF HEGAEFLGTE EYWSIIDIPS
GQLNGATGNV IVNEEDLSID GRGPGLGLSR TYNSLDSSDH LFGQGWYADA ETSVISTDGG
AMYIDEDATT HRFTKKADGT YQPPTGVYLE LTETADQFIL KTKDQTNAYF NKKGGKLQKV
VDGHNNATVY TYNDKNQLTA ITDASGRKLT FTYDENGHVT SITGPKNKKV TYSYENDLLK
KVTDTDGTVT SYDYDSEGRL VKQYSANSTE AKPVFTEYQY SGHRLEKAIN AKKETYVYSY
DADKKTLLMT QPNGRKVQYG YNEAGNPIQV IDDAEGLKIT TNTKYEGNNV VEDVDPNDVG
TGKATESYQY DKDGNVTSVK DAYGTETYEY NKNNDVTKMK DTEGNVTDIA YDGLDAVSET
DQSGKSSSAA VYDKYGNQIQ SSKDLSASTN ILKDGSFEAQ KSGWNLTASK DSGKISVIAD
KSGVLSGSKA LEVLSQSTSA GTDHGYSSAT QTVELEPNTT YTLSGKIKTD LAKSRAYFNI
DLRDKDQKRI QWIHNEYSAL AGKNDWTKRQ ITFTTPANAG KAVVYMEVDH KDKDGKGKAW
FDEVQLEKGE VSSSYNPVQN SSFTSATENW NVSGASVDSE EGFNDDVSLK AARTSASQAG
SVTKQTVVLG QSANDKPVYL TLTGMSKASS VKFTDEKDYS LQANVTYADG STGIYNAKFP
SGTQEWNRAA VVIPKTKPIN KVDISILFQK SATGTVWFDD IRLIEGSLLT KSTYDSNGNY
VTKEEDELGY ATSTDYDETG KKTSETDAKG EKTTYTYDQA DQLTNMTLSN GTSILHSYDK
EGNEVSKTIR AGADQTYKFE YDVMGKLVKT TDPLGNVLAS EYDANSNLTK TISPNGNEVS
LSYDGTDRVK SKSYNGTEKY IFTYDKNGNE TSVVNKEQNT TKKRTFDNKN RLTELTDRGG
SQTWTYPSDS DKLKTFSWIH GDQKGTNQFT YNKLDQMIEM KDSTSSYSFD YDENGNVQTF
ITGNGGGTSF SYDERNLVSS LHIGDKNGGD ILTESYEYDA NGNRTTINSS ASGKVQYEYG
KLNQLVKETH EDGTVIEYTY DGFGNRKTVT TIKDGSSKTV NASFNIMNQL TKVNDESISY
DKNGNRTSDG KFTYTWDAED NLTAVTKKGE DKPFATYKYD EKGNRIQKTV NGKVTNYFYD
GDSLNVLYET DADNNVTKSY TYGDSGQLLS YTENGKKYFY HYNAHGDIIA ISDSTGKTVA
KYQYDAWGNP TKTEASDEVK DNRYRYAGYQ YDEETGLYYL MARYYEPRNG VFLSLDPDPG
SDGDSLDQNG YAYGNNNPVM NVDPDGHWVW LVVNAGFAAY DGYKAYKSGK GWKGAAWAAA
SNFGPGKIFK GASRAYKFTK KAVKITGHTR HGLNQSIGRN GGRGVNLRAK LNAVRSPKKV
IKQPNGATKY VGKKATVVLN KRGKVITAYG SSRAKGSKHV FHTHGKGNKS KRRR
