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O05495

- YDHD_BACSU

UniProt

O05495 - YDHD_BACSU

Protein

Putative sporulation-specific glycosylase YdhD

Gene

ydhD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 99 (01 Oct 2014)
      Sequence version 2 (16 Jun 2009)
      Previous versions | rss
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    Functioni

    GO - Molecular functioni

    1. chitinase activity Source: InterPro

    GO - Biological processi

    1. chitin catabolic process Source: InterPro
    2. polysaccharide catabolic process Source: UniProtKB-KW
    3. sporulation resulting in formation of a cellular spore Source: UniProtKB-KW

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism, Polysaccharide degradation, Sporulation

    Enzyme and pathway databases

    BioCyciBSUB:BSU05710-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Putative sporulation-specific glycosylase YdhD (EC:3.2.-.-)
    Gene namesi
    Name:ydhD
    Ordered Locus Names:BSU05710
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001570: Chromosome

    Organism-specific databases

    GenoListiBSU05710.

    Subcellular locationi

    Spore wall 1 Publication
    Note: Probably localized either on the surface of the outer spore membrane and/or in the inner spore coat.

    GO - Cellular componenti

    1. spore wall Source: UniProtKB-SubCell

    Pathology & Biotechi

    Disruption phenotypei

    According to PubMed:11011148, cells show no effect vegetative growth, spore resistance to heat, chloroform and lysozyme, or spore germination in the presence of L-alanine. According to PubMed:12177332, cells have no detectable alteration in either dormant or germinating spore peptidoglycan, and germinate normally.2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 420420Putative sporulation-specific glycosylase YdhDPRO_0000227660Add
    BLAST

    Proteomic databases

    PaxDbiO05495.

    Expressioni

    Developmental stagei

    Expressed in the mother cell compartment from T2 of sporulation.

    Interactioni

    Protein-protein interaction databases

    STRINGi224308.BSU05710.

    Structurei

    Secondary structure

    1
    420
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi101 – 1099
    Helixi111 – 1133
    Beta strandi127 – 1359
    Helixi148 – 1569
    Beta strandi160 – 1667
    Helixi175 – 1828
    Helixi185 – 20218
    Beta strandi205 – 2106
    Helixi216 – 2183
    Helixi219 – 23517
    Beta strandi239 – 2457
    Helixi253 – 2553
    Helixi260 – 2667
    Beta strandi268 – 2736
    Helixi290 – 30011
    Turni301 – 3033
    Helixi306 – 3083
    Beta strandi309 – 3124
    Beta strandi317 – 3237
    Beta strandi331 – 3333
    Helixi335 – 34410
    Beta strandi350 – 3523
    Turni353 – 3564
    Beta strandi357 – 3637
    Beta strandi369 – 3735
    Helixi377 – 38913
    Beta strandi393 – 40210

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3CZ8X-ray2.20A/B96-402[»]
    ProteinModelPortaliO05495.
    SMRiO05495. Positions 2-403.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO05495.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Repeati4 – 4643LysM 1Add
    BLAST
    Repeati50 – 9344LysM 2Add
    BLAST

    Domaini

    LysM repeats are thought to be involved in peptidoglycan binding.

    Sequence similaritiesi

    Contains 2 LysM repeats.Curated

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiCOG3858.
    HOGENOMiHOG000056153.
    OrthoDBiEOG6S2686.
    PhylomeDBiO05495.

    Family and domain databases

    Gene3Di3.10.350.10. 2 hits.
    3.20.20.80. 1 hit.
    InterProiIPR011583. Chitinase_II.
    IPR001223. Glyco_hydro18cat.
    IPR013781. Glyco_hydro_catalytic_dom.
    IPR017853. Glycoside_hydrolase_SF.
    IPR018392. LysM_dom.
    [Graphical view]
    PfamiPF00704. Glyco_hydro_18. 1 hit.
    PF01476. LysM. 2 hits.
    [Graphical view]
    SMARTiSM00636. Glyco_18. 1 hit.
    SM00257. LysM. 2 hits.
    [Graphical view]
    SUPFAMiSSF51445. SSF51445. 2 hits.
    SSF54106. SSF54106. 2 hits.

    Sequencei

    Sequence statusi: Complete.

    O05495-1 [UniParc]FASTAAdd to Basket

    « Hide

    MFIHIVGPGD SLFSIGRRYG ASVDQIRGVN GLDETNIVPG QALLIPLYVY    50
    TVQPRDTLTA IAAKAFVPLE RLRAANPGIS PNALQAGAKI TIPSISNYIA 100
    GTLSFYVLRN PDLDRELIND YAPYSSSISI FEYHIAPNGD IANQLNDAAA 150
    IETTWQRRVT PLATITNLTS GGFSTEIVHQ VLNNPTARTN LVNNIYDLVS 200
    TRGYGGVTID FEQVSAADRD LFTGFLRQLR DRLQAGGYVL TIAVPAKTSD 250
    NIPWLRGYDY GGIGAVVNYM FIMAYDWHHA GSEPGPVAPI TEIRRTIEFT 300
    IAQVPSRKII IGVPLYGYDW IIPYQPGTVA SAISNQNAIE RAMRYQAPIQ 350
    YSAEYQSPFF RYSDQQGRTH EVWFEDVRSM SRKMQIVREY RLQAIGAWQL 400
    TLGFTPGPWL LRKFFTIRKV 420
    Length:420
    Mass (Da):46,864
    Last modified:June 16, 2009 - v2
    Checksum:i792B87B1BA04C79D
    GO

    Sequence cautioni

    The sequence BAA19695.1 differs from that shown. Reason: Frameshift at position 403.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D88802 Genomic DNA. Translation: BAA19695.1. Frameshift.
    AL009126 Genomic DNA. Translation: CAB12390.2.
    PIRiH69783.
    RefSeqiNP_388452.2. NC_000964.3.

    Genome annotation databases

    EnsemblBacteriaiCAB12390; CAB12390; BSU05710.
    GeneIDi939885.
    KEGGibsu:BSU05710.
    PATRICi18972756. VBIBacSub10457_0599.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D88802 Genomic DNA. Translation: BAA19695.1 . Frameshift.
    AL009126 Genomic DNA. Translation: CAB12390.2 .
    PIRi H69783.
    RefSeqi NP_388452.2. NC_000964.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3CZ8 X-ray 2.20 A/B 96-402 [» ]
    ProteinModelPortali O05495.
    SMRi O05495. Positions 2-403.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224308.BSU05710.

    Proteomic databases

    PaxDbi O05495.

    Protocols and materials databases

    DNASUi 939885.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB12390 ; CAB12390 ; BSU05710 .
    GeneIDi 939885.
    KEGGi bsu:BSU05710.
    PATRICi 18972756. VBIBacSub10457_0599.

    Organism-specific databases

    GenoListi BSU05710.

    Phylogenomic databases

    eggNOGi COG3858.
    HOGENOMi HOG000056153.
    OrthoDBi EOG6S2686.
    PhylomeDBi O05495.

    Enzyme and pathway databases

    BioCyci BSUB:BSU05710-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei O05495.

    Family and domain databases

    Gene3Di 3.10.350.10. 2 hits.
    3.20.20.80. 1 hit.
    InterProi IPR011583. Chitinase_II.
    IPR001223. Glyco_hydro18cat.
    IPR013781. Glyco_hydro_catalytic_dom.
    IPR017853. Glycoside_hydrolase_SF.
    IPR018392. LysM_dom.
    [Graphical view ]
    Pfami PF00704. Glyco_hydro_18. 1 hit.
    PF01476. LysM. 2 hits.
    [Graphical view ]
    SMARTi SM00636. Glyco_18. 1 hit.
    SM00257. LysM. 2 hits.
    [Graphical view ]
    SUPFAMi SSF51445. SSF51445. 2 hits.
    SSF54106. SSF54106. 2 hits.
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence and analysis of the phoB-rrnE-groESL region of the Bacillus subtilis chromosome."
      Sadaie Y., Yata K., Fujita M., Sagai H., Itaya M., Kasahara Y., Ogasawara N.
      Microbiology 143:1861-1866(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168 / JH642.
    2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    3. "From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later."
      Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A., Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.
      Microbiology 155:1758-1775(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: SEQUENCE REVISION TO C-TERMINUS.
    4. "Synthesis and characterization of the spore proteins of Bacillus subtilis YdhD, YkuD, and YkvP, which carry a motif conserved among cell wall binding proteins."
      Kodama T., Takamatsu H., Asai K., Ogasawara N., Sadaie Y., Watabe K.
      J. Biochem. 128:655-663(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, REGULATION, DISRUPTION PHENOTYPE, OVEREXPRESSION.
      Strain: 168.
    5. "Analysis of spore cortex lytic enzymes and related proteins in Bacillus subtilis endospore germination."
      Chirakkal H., O'Rourke M., Atrih A., Foster S.J., Moir A.
      Microbiology 148:2383-2392(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE.

    Entry informationi

    Entry nameiYDHD_BACSU
    AccessioniPrimary (citable) accession number: O05495
    Secondary accession number(s): Q797E8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 21, 2006
    Last sequence update: June 16, 2009
    Last modified: October 1, 2014
    This is version 99 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Transcription of ydhD is dependent on SigE.
    Cells producing excessive ydhD do not show impaired spore resistance, but their germination properties change: spores show reduced response to L-alanine and some of them germinate even without germinants.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. Glycosyl hydrolases
      Classification of glycosyl hydrolase families and list of entries
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3