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O34816 (YKUD_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 66. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Putative L,D-transpeptidase YkuD
EC=2.-.-.-
Alternative name(s):
Spore protein YkuD
Gene names
Name:ykuD
Ordered Locus Names:BSU14040
OrganismBacillus subtilis
Taxonomic identifier1423 [NCBI]
Taxonomic lineageBacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length164 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Probable enzyme that may play an important role in cell wall biology. Ref.4

Pathway

Cell wall biogenesis; peptidoglycan biosynthesis.

Subunit structure

Monomer. Ref.4

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.3

Developmental stage

Expressed in the mother cell compartment from T4 of sporulation.

Domain

LysM repeats are thought to be involved in peptidoglycan binding.

Miscellaneous

Regulated by sigK. Could also be negatively regulated by gerE. Transcribed by sigK RNA polymerase.

Inactivation of the ykuD gene does not affect vegetative growth, spore resistance to heat, chloroform and lysozyme, or spore germination in the presence of L-alanine.

Sequence similarities

Belongs to the YkuD family.

Contains 1 LysM repeat.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 164164Putative L,D-transpeptidase YkuD
PRO_0000227661

Regions

Repeat4 – 4643LysM

Secondary structure

1 ................................... 164
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O34816 [UniParc].

Last modified January 1, 1998. Version 1.
Checksum: 6E13A750890E7F4C

FASTA16417,643
        10         20         30         40         50         60 
MLTYQVKQGD TLNSIAADFR ISTAALLQAN PSLQAGLTAG QSIVIPGLPD PYTIPYHIAV 

        70         80         90        100        110        120 
SIGAKTLTLS LNNRVMKTYP IAVGKILTQT PTGEFYIINR QRNPGGPFGA YWLSLSKQHY 

       130        140        150        160 
GIHGTNNPAS IGKAVSKGCI RMHNKDVIEL ASIVPNGTRV TINR

« Hide

References

« Hide 'large scale' references
[1]"Sequence of the Bacillus subtilis chromosome from ykuA to cse-15."
Scanlan E., Devine K.M.
Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: 168.
[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: 9384377] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: 168.
[3]"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: 11011148] [Abstract]
Cited for: SUBCELLULAR LOCATION, REGULATION, EXPRESSION.
Strain: 168.
[4]"B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes."
Bielnicki J., Devedjiev Y., Derewenda U., Dauter Z., Joachimiak A., Derewenda Z.S.
Proteins 62:144-151(2006) [PubMed: 16287140] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), SUBUNIT, FUNCTION.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AJ222587 Genomic DNA. Translation: CAA10867.1.
AL009126 Genomic DNA. Translation: CAB13277.1.
PIRA69865.
RefSeqNP_389287.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1Y7MX-ray2.05A/B1-164[»]
ProteinModelPortalO34816.
SMRO34816. Positions 1-164.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaEBBACT00000002362; EBBACP00000002362; EBBACG00000002357.
GeneID939216.
GenomeReviewsGene locus BSU14040 in contig AL009126_GR.
KEGGbsu:BSU14040.
NMPDRfig|224308.1.peg.1406.
PATRIC18974593. VBIBacSub10457_1488.

Organism-specific databases

GenoListBSU14040.

Phylogenomic databases

GeneTreeEBGT00070000032370.
HOGENOMHBG295778.
OMAKGCIRMH.
PhylomeDBO34816.
ProtClustDBCLSK887215.

Enzyme and pathway databases

BioCycBSUB:BSU14040-MONOMER.

Family and domain databases

InterProIPR005490. LD_TPept_cat_dom.
IPR018392. Peptidoglycan-bd_lysin.
IPR002482. Peptidoglycan-bd_Lysin_subgr.
[Graphical view]
PfamPF01476. LysM. 1 hit.
PF03734. YkuD. 1 hit.
[Graphical view]
SMARTSM00257. LysM. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameYKUD_BACSU
AccessionPrimary (citable) accession number: O34816
Secondary accession number(s): Q796K7
Entry history
Integrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: January 1, 1998
Last modified: January 25, 2012
This is version 66 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Bacillus subtilis

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

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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