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Protein

Putative sporulation-specific glycosylase YdhD

Gene

ydhD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: 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 Componenti: Chromosome

Organism-specific databases

GenoListiBSU05710.

Subcellular locationi

  1. Spore wall 1 Publication

  2. 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
Complete GO annotation...

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 – 1099Combined sources
Helixi111 – 1133Combined sources
Beta strandi127 – 1359Combined sources
Helixi148 – 1569Combined sources
Beta strandi160 – 1667Combined sources
Helixi175 – 1828Combined sources
Helixi185 – 20218Combined sources
Beta strandi205 – 2106Combined sources
Helixi216 – 2183Combined sources
Helixi219 – 23517Combined sources
Beta strandi239 – 2457Combined sources
Helixi253 – 2553Combined sources
Helixi260 – 2667Combined sources
Beta strandi268 – 2736Combined sources
Helixi290 – 30011Combined sources
Turni301 – 3033Combined sources
Helixi306 – 3083Combined sources
Beta strandi309 – 3124Combined sources
Beta strandi317 – 3237Combined sources
Beta strandi331 – 3333Combined sources
Helixi335 – 34410Combined sources
Beta strandi350 – 3523Combined sources
Turni353 – 3564Combined sources
Beta strandi357 – 3637Combined sources
Beta strandi369 – 3735Combined sources
Helixi377 – 38913Combined sources
Beta strandi393 – 40210Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
InParanoidiO05495.
OMAiMFIMAYD.
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

        10         20         30         40         50
MFIHIVGPGD SLFSIGRRYG ASVDQIRGVN GLDETNIVPG QALLIPLYVY
60 70 80 90 100
TVQPRDTLTA IAAKAFVPLE RLRAANPGIS PNALQAGAKI TIPSISNYIA
110 120 130 140 150
GTLSFYVLRN PDLDRELIND YAPYSSSISI FEYHIAPNGD IANQLNDAAA
160 170 180 190 200
IETTWQRRVT PLATITNLTS GGFSTEIVHQ VLNNPTARTN LVNNIYDLVS
210 220 230 240 250
TRGYGGVTID FEQVSAADRD LFTGFLRQLR DRLQAGGYVL TIAVPAKTSD
260 270 280 290 300
NIPWLRGYDY GGIGAVVNYM FIMAYDWHHA GSEPGPVAPI TEIRRTIEFT
310 320 330 340 350
IAQVPSRKII IGVPLYGYDW IIPYQPGTVA SAISNQNAIE RAMRYQAPIQ
360 370 380 390 400
YSAEYQSPFF RYSDQQGRTH EVWFEDVRSM SRKMQIVREY RLQAIGAWQL
410 420
TLGFTPGPWL LRKFFTIRKV
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. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
Links Updated
D88802 Genomic DNA. Translation: BAA19695.1. Frameshift.
AL009126 Genomic DNA. Translation: CAB12390.2.
PIRiH69783.
RefSeqiNP_388452.2. NC_000964.3.

3D structure databases

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

Protein-protein interaction databases

STRINGi224308.BSU05710.

Proteomic databases

PaxDbiO05495.

Protocols and materials databases

DNASUi939885.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

GenoListiBSU05710.

Phylogenomic databases

eggNOGiCOG3858.
HOGENOMiHOG000056153.
InParanoidiO05495.
OMAiMFIMAYD.
OrthoDBiEOG6S2686.
PhylomeDBiO05495.

Enzyme and pathway databases

BioCyciBSUB:BSU05710-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO05495.

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.
ProtoNetiSearch...

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: January 7, 2015
This is version 101 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.