ID   YDHD_BACSU              Reviewed;         420 AA.
AC   O05495; Q797E8;
DT   21-MAR-2006, integrated into UniProtKB/Swiss-Prot.
DT   16-JUN-2009, sequence version 2.
DT   27-MAR-2024, entry version 143.
DE   RecName: Full=Putative sporulation-specific glycosylase YdhD;
DE            EC=3.2.-.-;
GN   Name=ydhD; OrderedLocusNames=BSU05710;
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 / JH642;
RX   PubMed=9202461; DOI=10.1099/00221287-143-6-1861;
RA   Sadaie Y., Yata K., Fujita M., Sagai H., Itaya M., Kasahara Y.,
RA   Ogasawara N.;
RT   "Nucleotide sequence and analysis of the phoB-rrnE-groESL region of the
RT   Bacillus subtilis chromosome.";
RL   Microbiology 143:1861-1866(1997).
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   SEQUENCE REVISION TO C-TERMINUS.
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   [4]
RP   SUBCELLULAR LOCATION, REGULATION, DISRUPTION PHENOTYPE, AND OVEREXPRESSION.
RC   STRAIN=168;
RX   PubMed=11011148; DOI=10.1093/oxfordjournals.jbchem.a022798;
RA   Kodama T., Takamatsu H., Asai K., Ogasawara N., Sadaie Y., Watabe K.;
RT   "Synthesis and characterization of the spore proteins of Bacillus subtilis
RT   YdhD, YkuD, and YkvP, which carry a motif conserved among cell wall binding
RT   proteins.";
RL   J. Biochem. 128:655-663(2000).
RN   [5]
RP   DISRUPTION PHENOTYPE.
RX   PubMed=12177332; DOI=10.1099/00221287-148-8-2383;
RA   Chirakkal H., O'Rourke M., Atrih A., Foster S.J., Moir A.;
RT   "Analysis of spore cortex lytic enzymes and related proteins in Bacillus
RT   subtilis endospore germination.";
RL   Microbiology 148:2383-2392(2002).
CC   -!- SUBCELLULAR LOCATION: Spore wall {ECO:0000305|PubMed:11011148}.
CC       Note=Probably localized either on the surface of the outer spore
CC       membrane and/or in the inner spore coat.
CC   -!- DEVELOPMENTAL STAGE: Expressed in the mother cell compartment from T2
CC       of sporulation.
CC   -!- DOMAIN: LysM domains are thought to be involved in peptidoglycan
CC       binding.
CC   -!- DISRUPTION PHENOTYPE: According to PubMed:11011148, cells show no
CC       effect vegetative growth, spore resistance to heat, chloroform and
CC       lysozyme, or spore germination in the presence of L-alanine. According
CC       to PubMed:12177332, cells have no detectable alteration in either
CC       dormant or germinating spore peptidoglycan, and germinate normally.
CC       {ECO:0000269|PubMed:11011148, ECO:0000269|PubMed:12177332}.
CC   -!- MISCELLANEOUS: Transcription of ydhD is dependent on SigE.
CC   -!- MISCELLANEOUS: Cells producing excessive ydhD do not show impaired
CC       spore resistance, but their germination properties change: spores show
CC       reduced response to L-alanine and some of them germinate even without
CC       germinants.
CC   -!- SIMILARITY: Belongs to the glycosyl hydrolase 18 family. Chitinase
CC       class II subfamily. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAA19695.1; Type=Frameshift; Evidence={ECO:0000305};
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DR   EMBL; D88802; BAA19695.1; ALT_FRAME; Genomic_DNA.
DR   EMBL; AL009126; CAB12390.2; -; Genomic_DNA.
DR   PIR; H69783; H69783.
DR   RefSeq; NP_388452.2; NC_000964.3.
DR   RefSeq; WP_003234126.1; NZ_JNCM01000031.1.
DR   PDB; 3CZ8; X-ray; 2.20 A; A/B=96-402.
DR   PDBsum; 3CZ8; -.
DR   AlphaFoldDB; O05495; -.
DR   SMR; O05495; -.
DR   STRING; 224308.BSU05710; -.
DR   CAZy; CBM50; Carbohydrate-Binding Module Family 50.
DR   CAZy; GH18; Glycoside Hydrolase Family 18.
DR   PaxDb; 224308-BSU05710; -.
DR   DNASU; 939885; -.
DR   EnsemblBacteria; CAB12390; CAB12390; BSU_05710.
DR   GeneID; 939885; -.
DR   KEGG; bsu:BSU05710; -.
DR   PATRIC; fig|224308.179.peg.614; -.
DR   eggNOG; COG1388; Bacteria.
DR   eggNOG; COG3858; Bacteria.
DR   InParanoid; O05495; -.
DR   OrthoDB; 9769314at2; -.
DR   PhylomeDB; O05495; -.
DR   BioCyc; BSUB:BSU05710-MONOMER; -.
DR   EvolutionaryTrace; O05495; -.
DR   Proteomes; UP000001570; Chromosome.
DR   GO; GO:0031160; C:spore wall; IEA:UniProtKB-SubCell.
DR   GO; GO:0008061; F:chitin binding; IEA:InterPro.
DR   GO; GO:0016798; F:hydrolase activity, acting on glycosyl bonds; IEA:UniProtKB-KW.
DR   GO; GO:0009313; P:oligosaccharide catabolic process; IBA:GO_Central.
DR   GO; GO:0000272; P:polysaccharide catabolic process; IEA:UniProtKB-KW.
DR   GO; GO:0030435; P:sporulation resulting in formation of a cellular spore; IEA:UniProtKB-KW.
DR   CDD; cd02874; GH18_CFLE_spore_hydrolase; 1.
DR   CDD; cd00118; LysM; 2.
DR   Gene3D; 3.10.50.10; -; 1.
DR   Gene3D; 3.20.20.80; Glycosidases; 1.
DR   Gene3D; 3.10.350.10; LysM domain; 2.
DR   InterPro; IPR041704; CFLE_GH18.
DR   InterPro; IPR011583; Chitinase_II.
DR   InterPro; IPR029070; Chitinase_insertion_sf.
DR   InterPro; IPR001223; Glyco_hydro18_cat.
DR   InterPro; IPR017853; Glycoside_hydrolase_SF.
DR   InterPro; IPR018392; LysM_dom.
DR   InterPro; IPR036779; LysM_dom_sf.
DR   PANTHER; PTHR46290; DI-N-ACETYLCHITOBIASE; 1.
DR   PANTHER; PTHR46290:SF1; DI-N-ACETYLCHITOBIASE; 1.
DR   Pfam; PF00704; Glyco_hydro_18; 1.
DR   Pfam; PF01476; LysM; 2.
DR   SMART; SM00636; Glyco_18; 1.
DR   SMART; SM00257; LysM; 2.
DR   SUPFAM; SSF51445; (Trans)glycosidases; 1.
DR   SUPFAM; SSF54106; LysM domain; 2.
DR   PROSITE; PS51910; GH18_2; 1.
DR   PROSITE; PS51782; LYSM; 2.
PE   1: Evidence at protein level;
KW   3D-structure; Carbohydrate metabolism; Glycosidase; Hydrolase;
KW   Polysaccharide degradation; Reference proteome; Repeat; Sporulation.
FT   CHAIN           1..420
FT                   /note="Putative sporulation-specific glycosylase YdhD"
FT                   /id="PRO_0000227660"
FT   DOMAIN          2..45
FT                   /note="LysM 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01118"
FT   DOMAIN          48..92
FT                   /note="LysM 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01118"
FT   DOMAIN          100..420
FT                   /note="GH18"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01258"
FT   ACT_SITE        212
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01258"
FT   STRAND          101..109
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   HELIX           111..113
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   STRAND          127..135
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   HELIX           148..156
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   STRAND          160..166
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   HELIX           175..182
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   HELIX           185..202
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   STRAND          205..210
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   HELIX           216..218
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   HELIX           219..235
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   STRAND          239..245
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   HELIX           253..255
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   HELIX           260..266
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   STRAND          268..273
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   HELIX           290..300
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   TURN            301..303
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   HELIX           306..308
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   STRAND          309..312
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   STRAND          317..323
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   STRAND          331..333
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   HELIX           335..344
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   STRAND          350..352
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   TURN            353..356
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   STRAND          357..363
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   STRAND          369..373
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   HELIX           377..389
FT                   /evidence="ECO:0007829|PDB:3CZ8"
FT   STRAND          393..402
FT                   /evidence="ECO:0007829|PDB:3CZ8"
SQ   SEQUENCE   420 AA;  46864 MW;  792B87B1BA04C79D CRC64;
     MFIHIVGPGD SLFSIGRRYG ASVDQIRGVN GLDETNIVPG QALLIPLYVY TVQPRDTLTA
     IAAKAFVPLE RLRAANPGIS PNALQAGAKI TIPSISNYIA GTLSFYVLRN PDLDRELIND
     YAPYSSSISI FEYHIAPNGD IANQLNDAAA IETTWQRRVT PLATITNLTS GGFSTEIVHQ
     VLNNPTARTN LVNNIYDLVS TRGYGGVTID FEQVSAADRD LFTGFLRQLR DRLQAGGYVL
     TIAVPAKTSD NIPWLRGYDY GGIGAVVNYM FIMAYDWHHA GSEPGPVAPI TEIRRTIEFT
     IAQVPSRKII IGVPLYGYDW IIPYQPGTVA SAISNQNAIE RAMRYQAPIQ YSAEYQSPFF
     RYSDQQGRTH EVWFEDVRSM SRKMQIVREY RLQAIGAWQL TLGFTPGPWL LRKFFTIRKV
//