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O05495 (YDHD_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 97. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Putative sporulation-specific glycosylase YdhD

EC=3.2.-.-
Gene names
Name:ydhD
Ordered Locus Names:BSU05710
OrganismBacillus subtilis (strain 168) [Reference proteome] [HAMAP]
Taxonomic identifier224308 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Protein attributes

Sequence length420 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Subcellular location

Spore wall Probable. Note: Probably localized either on the surface of the outer spore membrane and/or in the inner spore coat. Ref.4

Developmental stage

Expressed in the mother cell compartment from T2 of sporulation.

Domain

LysM repeats are thought to be involved in peptidoglycan binding.

Disruption phenotype

According to Ref.4, cells show no effect vegetative growth, spore resistance to heat, chloroform and lysozyme, or spore germination in the presence of L-alanine. According to Ref.5, cells have no detectable alteration in either dormant or germinating spore peptidoglycan, and germinate normally. Ref.4 Ref.5

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.

Sequence similarities

Belongs to the glycosyl hydrolase 18 family. Chitinase class II subfamily.

Contains 2 LysM repeats.

Sequence caution

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 420420Putative sporulation-specific glycosylase YdhD
PRO_0000227660

Regions

Repeat4 – 4643LysM 1
Repeat50 – 9344LysM 2

Secondary structure

.................................................. 420
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O05495 [UniParc].

Last modified June 16, 2009. Version 2.
Checksum: 792B87B1BA04C79D

FASTA42046,864
        10         20         30         40         50         60 
MFIHIVGPGD SLFSIGRRYG ASVDQIRGVN GLDETNIVPG QALLIPLYVY TVQPRDTLTA 

        70         80         90        100        110        120 
IAAKAFVPLE RLRAANPGIS PNALQAGAKI TIPSISNYIA GTLSFYVLRN PDLDRELIND 

       130        140        150        160        170        180 
YAPYSSSISI FEYHIAPNGD IANQLNDAAA IETTWQRRVT PLATITNLTS GGFSTEIVHQ 

       190        200        210        220        230        240 
VLNNPTARTN LVNNIYDLVS TRGYGGVTID FEQVSAADRD LFTGFLRQLR DRLQAGGYVL 

       250        260        270        280        290        300 
TIAVPAKTSD NIPWLRGYDY GGIGAVVNYM FIMAYDWHHA GSEPGPVAPI TEIRRTIEFT 

       310        320        330        340        350        360 
IAQVPSRKII IGVPLYGYDW IIPYQPGTVA SAISNQNAIE RAMRYQAPIQ YSAEYQSPFF 

       370        380        390        400        410        420 
RYSDQQGRTH EVWFEDVRSM SRKMQIVREY RLQAIGAWQL TLGFTPGPWL LRKFFTIRKV 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D88802 Genomic DNA. Translation: BAA19695.1. Frameshift.
AL009126 Genomic DNA. Translation: CAB12390.2.
PIRH69783.
RefSeqNP_388452.2. NC_000964.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3CZ8X-ray2.20A/B96-402[»]
ProteinModelPortalO05495.
SMRO05495. Positions 2-403.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING224308.BSU05710.

Proteomic databases

PaxDbO05495.

Protocols and materials databases

DNASU939885.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAB12390; CAB12390; BSU05710.
GeneID939885.
KEGGbsu:BSU05710.
PATRIC18972756. VBIBacSub10457_0599.

Organism-specific databases

GenoListBSU05710.

Phylogenomic databases

eggNOGCOG3858.
HOGENOMHOG000056153.
OrthoDBEOG6S2686.
PhylomeDBO05495.

Enzyme and pathway databases

BioCycBSUB:BSU05710-MONOMER.

Family and domain databases

Gene3D3.10.350.10. 2 hits.
3.20.20.80. 1 hit.
InterProIPR011583. Chitinase_II.
IPR001223. Glyco_hydro18cat.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
IPR018392. LysM_dom.
[Graphical view]
PfamPF00704. Glyco_hydro_18. 1 hit.
PF01476. LysM. 2 hits.
[Graphical view]
SMARTSM00636. Glyco_18. 1 hit.
SM00257. LysM. 2 hits.
[Graphical view]
SUPFAMSSF51445. SSF51445. 2 hits.
SSF54106. SSF54106. 2 hits.
ProtoNetSearch...

Other

EvolutionaryTraceO05495.

Entry information

Entry nameYDHD_BACSU
AccessionPrimary (citable) accession number: O05495
Secondary accession number(s): Q797E8
Entry history
Integrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: June 16, 2009
Last modified: July 9, 2014
This is version 97 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Glycosyl hydrolases

Classification of glycosyl hydrolase families and list of entries

Bacillus subtilis

Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList