YDHD_BACSU
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 03-AUG-2022, entry version 135.
DE RecName: Full=Putative sporulation-specific glycosylase YdhD;
DE EC=3.2.-.-;
GN Name=ydhD; OrderedLocusNames=BSU05710;
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 / 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 RefSeq; WP_009966675.1; NZ_CM000487.1.
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; O05495; -.
DR PRIDE; O05495; -.
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 OMA; MRYQSPI; -.
DR PhylomeDB; O05495; -.
DR BioCyc; BSUB:BSU05710-MON; -.
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; 3.10.350.10; -; 2.
DR Gene3D; 3.10.50.10; -; 1.
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 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; SSF51445; 1.
DR SUPFAM; SSF54106; SSF54106; 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
