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O05495

- YDHD_BACSU

UniProt

O05495 - YDHD_BACSU

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Protein
Putative sporulation-specific glycosylase YdhD
Gene
ydhD, BSU05710
Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 3 out of 5 - Experimental evidence at protein leveli

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
Complete GO annotation...

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

GO - Cellular componenti

  1. spore wall Source: UniProtKB-SubCell
Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

According to 1 Publication, cells show no effect vegetative growth, spore resistance to heat, chloroform and lysozyme, or spore germination in the presence of L-alanine. According to 1 Publication, 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 YdhD
PRO_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

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.

Miscellaneous databases

EvolutionaryTraceiO05495.

Family & Domainsi

Domains and Repeats

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

Domaini

LysM repeats are thought to be involved in peptidoglycan binding.

Sequence similaritiesi

Contains 2 LysM repeats.

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 98 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

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