YKUD_BACSU
ID YKUD_BACSU Reviewed; 164 AA.
AC O34816; Q796K7;
DT 21-MAR-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Putative L,D-transpeptidase YkuD;
DE EC=2.-.-.-;
DE AltName: Full=Spore protein YkuD;
GN Name=ykuD; OrderedLocusNames=BSU14040;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RA Scanlan E., Devine K.M.;
RT "Sequence of the Bacillus subtilis chromosome from ykuA to cse-15.";
RL Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP SUBCELLULAR LOCATION, REGULATION, AND EXPRESSION.
RC STRAIN=168;
RX PubMed=11011148; DOI=10.1093/oxfordjournals.jbchem.a022798;
RA Kodama T., Takamatsu H., Asai K., Ogasawara N., Sadaie Y., Watabe K.;
RT "Synthesis and characterization of the spore proteins of Bacillus subtilis
RT YdhD, YkuD, and YkvP, which carry a motif conserved among cell wall binding
RT proteins.";
RL J. Biochem. 128:655-663(2000).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), SUBUNIT, AND FUNCTION.
RX PubMed=16287140; DOI=10.1002/prot.20702;
RA Bielnicki J., Devedjiev Y., Derewenda U., Dauter Z., Joachimiak A.,
RA Derewenda Z.S.;
RT "B. subtilis ykuD protein at 2.0 A resolution: insights into the structure
RT and function of a novel, ubiquitous family of bacterial enzymes.";
RL Proteins 62:144-151(2006).
CC -!- FUNCTION: Probable enzyme that may play an important role in cell wall
CC biology. {ECO:0000269|PubMed:16287140}.
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:16287140}.
CC -!- SUBCELLULAR LOCATION: Spore wall {ECO:0000305|PubMed:11011148}.
CC Note=Probably localized either on the surface of the outer spore
CC membrane and/or in the inner spore coat.
CC -!- DEVELOPMENTAL STAGE: Expressed in the mother cell compartment from T4
CC of sporulation.
CC -!- DOMAIN: LysM domains are thought to be involved in peptidoglycan
CC binding.
CC -!- MISCELLANEOUS: Regulated by SigK. Could also be negatively regulated by
CC GerE. Transcribed by SigK RNA polymerase.
CC -!- MISCELLANEOUS: Inactivation of the ykuD gene does not affect vegetative
CC growth, spore resistance to heat, chloroform and lysozyme, or spore
CC germination in the presence of L-alanine.
CC -!- SIMILARITY: Belongs to the YkuD family. {ECO:0000305}.
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DR EMBL; AJ222587; CAA10867.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13277.1; -; Genomic_DNA.
DR PIR; A69865; A69865.
DR RefSeq; NP_389287.1; NC_000964.3.
DR RefSeq; WP_010886500.1; NZ_JNCM01000035.1.
DR PDB; 1Y7M; X-ray; 2.05 A; A/B=1-164.
DR PDB; 2MTZ; NMR; -; A=2-164.
DR PDB; 3ZQD; NMR; -; A=2-164.
DR PDB; 4A1I; X-ray; 1.76 A; A/B/C/D/E/F/G/H=1-164.
DR PDB; 4A1J; X-ray; 2.20 A; A/B=1-164.
DR PDB; 4A1K; X-ray; 1.75 A; A=1-164.
DR PDB; 4A52; NMR; -; A=2-164.
DR PDBsum; 1Y7M; -.
DR PDBsum; 2MTZ; -.
DR PDBsum; 3ZQD; -.
DR PDBsum; 4A1I; -.
DR PDBsum; 4A1J; -.
DR PDBsum; 4A1K; -.
DR PDBsum; 4A52; -.
DR AlphaFoldDB; O34816; -.
DR BMRB; O34816; -.
DR SMR; O34816; -.
DR STRING; 224308.BSU14040; -.
DR CAZy; CBM50; Carbohydrate-Binding Module Family 50.
DR MEROPS; C82.003; -.
DR PaxDb; O34816; -.
DR PRIDE; O34816; -.
DR EnsemblBacteria; CAB13277; CAB13277; BSU_14040.
DR GeneID; 939216; -.
DR KEGG; bsu:BSU14040; -.
DR PATRIC; fig|224308.43.peg.1488; -.
DR eggNOG; COG1376; Bacteria.
DR InParanoid; O34816; -.
DR OMA; FGAYWLS; -.
DR PhylomeDB; O34816; -.
DR BioCyc; BSUB:BSU14040-MON; -.
DR UniPathway; UPA00219; -.
DR EvolutionaryTrace; O34816; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0031160; C:spore wall; IEA:UniProtKB-SubCell.
DR GO; GO:0016757; F:glycosyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0071972; F:peptidoglycan L,D-transpeptidase activity; IBA:GO_Central.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0018104; P:peptidoglycan-protein cross-linking; IBA:GO_Central.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR GO; GO:0030435; P:sporulation resulting in formation of a cellular spore; IEA:UniProtKB-KW.
DR CDD; cd00118; LysM; 1.
DR CDD; cd16913; YkuD_like; 1.
DR Gene3D; 2.40.440.10; -; 1.
DR Gene3D; 3.10.350.10; -; 1.
DR InterPro; IPR005490; LD_TPept_cat_dom.
DR InterPro; IPR018392; LysM_dom.
DR InterPro; IPR036779; LysM_dom_sf.
DR InterPro; IPR038063; Transpep_catalytic_dom.
DR Pfam; PF01476; LysM; 1.
DR Pfam; PF03734; YkuD; 1.
DR SMART; SM00257; LysM; 1.
DR SUPFAM; SSF141523; SSF141523; 1.
DR SUPFAM; SSF54106; SSF54106; 1.
DR PROSITE; PS51782; LYSM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell shape; Cell wall biogenesis/degradation;
KW Glycosyltransferase; Hydrolase; Peptidoglycan synthesis;
KW Reference proteome; Sporulation; Transferase.
FT CHAIN 1..164
FT /note="Putative L,D-transpeptidase YkuD"
FT /id="PRO_0000227661"
FT DOMAIN 2..45
FT /note="LysM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01118"
FT STRAND 2..5
FT /evidence="ECO:0007829|PDB:4A1K"
FT HELIX 12..18
FT /evidence="ECO:0007829|PDB:4A1K"
FT HELIX 23..29
FT /evidence="ECO:0007829|PDB:4A1K"
FT HELIX 31..35
FT /evidence="ECO:0007829|PDB:4A1K"
FT STRAND 42..45
FT /evidence="ECO:0007829|PDB:4A1K"
FT HELIX 51..53
FT /evidence="ECO:0007829|PDB:4A1K"
FT STRAND 56..61
FT /evidence="ECO:0007829|PDB:4A1K"
FT TURN 62..65
FT /evidence="ECO:0007829|PDB:4A1K"
FT STRAND 66..71
FT /evidence="ECO:0007829|PDB:4A1K"
FT STRAND 74..80
FT /evidence="ECO:0007829|PDB:4A1K"
FT STRAND 82..84
FT /evidence="ECO:0007829|PDB:4A1K"
FT HELIX 86..88
FT /evidence="ECO:0007829|PDB:4A1K"
FT STRAND 93..102
FT /evidence="ECO:0007829|PDB:4A1K"
FT HELIX 106..108
FT /evidence="ECO:0007829|PDB:4A1K"
FT STRAND 111..117
FT /evidence="ECO:0007829|PDB:4A1K"
FT STRAND 121..123
FT /evidence="ECO:0007829|PDB:4A1K"
FT HELIX 128..130
FT /evidence="ECO:0007829|PDB:4A1K"
FT STRAND 133..141
FT /evidence="ECO:0007829|PDB:4A1K"
FT HELIX 144..153
FT /evidence="ECO:0007829|PDB:4A1K"
FT STRAND 159..163
FT /evidence="ECO:0007829|PDB:4A1K"
SQ SEQUENCE 164 AA; 17643 MW; 6E13A750890E7F4C CRC64;
MLTYQVKQGD TLNSIAADFR ISTAALLQAN PSLQAGLTAG QSIVIPGLPD PYTIPYHIAV
SIGAKTLTLS LNNRVMKTYP IAVGKILTQT PTGEFYIINR QRNPGGPFGA YWLSLSKQHY
GIHGTNNPAS IGKAVSKGCI RMHNKDVIEL ASIVPNGTRV TINR
