ID A0A4Y7RDI8_9FIRM Unreviewed; 312 AA.
AC A0A4Y7RDI8;
DT 18-SEP-2019, integrated into UniProtKB/TrEMBL.
DT 18-SEP-2019, sequence version 1.
DT 02-APR-2025, entry version 20.
DE SubName: Full=Putative L,D-transpeptidase YkuD {ECO:0000313|EMBL:TEB07078.1};
DE EC=2.-.-.- {ECO:0000313|EMBL:TEB07078.1};
GN Name=ykuD_1 {ECO:0000313|EMBL:TEB07078.1};
GN ORFNames=Psch_00619 {ECO:0000313|EMBL:TEB07078.1};
OS Pelotomaculum schinkii.
OC Bacteria; Bacillati; Bacillota; Clostridia; Eubacteriales;
OC Desulfotomaculaceae; Pelotomaculum.
OX NCBI_TaxID=78350 {ECO:0000313|EMBL:TEB07078.1, ECO:0000313|Proteomes:UP000298324};
RN [1] {ECO:0000313|EMBL:TEB07078.1, ECO:0000313|Proteomes:UP000298324}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=HH {ECO:0000313|EMBL:TEB07078.1,
RC ECO:0000313|Proteomes:UP000298324};
RX PubMed=30126076; DOI=.1111/1462-2920.14388;
RA Hidalgo-Ahumada C.A.P., Nobu M.K., Narihiro T., Tamaki H., Liu W.T.,
RA Kamagata Y., Stams A.J.M., Imachi H., Sousa D.Z.;
RT "Novel energy conservation strategies and behaviour of Pelotomaculum
RT schinkii driving syntrophic propionate catabolism.";
RL Environ. Microbiol. 20:4503-4511(2018).
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC {ECO:0000256|ARBA:ARBA00004752, ECO:0000256|PROSITE-ProRule:PRU01373}.
CC -!- SIMILARITY: Belongs to the YkuD family.
CC {ECO:0000256|ARBA:ARBA00005992}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:TEB07078.1}.
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DR EMBL; QFGA01000001; TEB07078.1; -; Genomic_DNA.
DR RefSeq; WP_134217379.1; NZ_QFGA01000001.1.
DR AlphaFoldDB; A0A4Y7RDI8; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000298324; Unassembled WGS sequence.
DR GO; GO:0005576; C:extracellular region; IEA:TreeGrafter.
DR GO; GO:0016757; F:glycosyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0071972; F:peptidoglycan L,D-transpeptidase activity; IEA:TreeGrafter.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-UniRule.
DR GO; GO:0018104; P:peptidoglycan-protein cross-linking; IEA:TreeGrafter.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-UniRule.
DR CDD; cd16913; YkuD_like; 1.
DR Gene3D; 2.40.440.10; L,D-transpeptidase catalytic domain-like; 1.
DR Gene3D; 1.10.101.10; PGBD-like superfamily/PGBD; 2.
DR InterPro; IPR050979; LD-transpeptidase.
DR InterPro; IPR005490; LD_TPept_cat_dom.
DR InterPro; IPR002477; Peptidoglycan-bd-like.
DR InterPro; IPR036365; PGBD-like_sf.
DR InterPro; IPR036366; PGBDSf.
DR InterPro; IPR038063; Transpep_catalytic_dom.
DR PANTHER; PTHR30582; L,D-TRANSPEPTIDASE; 1.
DR PANTHER; PTHR30582:SF24; L,D-TRANSPEPTIDASE ERFK_SRFK-RELATED; 1.
DR Pfam; PF01471; PG_binding_1; 2.
DR Pfam; PF03734; YkuD; 1.
DR SUPFAM; SSF141523; L,D-transpeptidase catalytic domain-like; 1.
DR SUPFAM; SSF47090; PGBD-like; 2.
DR PROSITE; PS52029; LD_TPASE; 1.
PE 3: Inferred from homology;
KW Cell shape {ECO:0000256|ARBA:ARBA00022960, ECO:0000256|PROSITE-
KW ProRule:PRU01373};
KW Cell wall biogenesis/degradation {ECO:0000256|ARBA:ARBA00023316,
KW ECO:0000256|PROSITE-ProRule:PRU01373};
KW Glycosyltransferase {ECO:0000256|ARBA:ARBA00022676};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801};
KW Peptidoglycan synthesis {ECO:0000256|ARBA:ARBA00022984,
KW ECO:0000256|PROSITE-ProRule:PRU01373};
KW Reference proteome {ECO:0000313|Proteomes:UP000298324};
KW Signal {ECO:0000256|SAM:SignalP};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000313|EMBL:TEB07078.1}.
FT SIGNAL 1..26
FT /evidence="ECO:0000256|SAM:SignalP"
FT CHAIN 27..312
FT /evidence="ECO:0000256|SAM:SignalP"
FT /id="PRO_5021192838"
FT DOMAIN 126..235
FT /note="L,D-TPase catalytic"
FT /evidence="ECO:0000259|PROSITE:PS52029"
FT ACT_SITE 195
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01373"
FT ACT_SITE 211
FT /note="Nucleophile"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01373"
SQ SEQUENCE 312 AA; 33852 MW; 47995CDE35C2438F CRC64;
MNYSRLGAAT FAFVFFCFAL TSTSEALQNL ACPLNPEQGR VLFLKEPNIS GRDVAELQER
LKALGYYKGA INSVYNDETS RAVASAQENL DLHPNGTVDH VTLQALVAAT DQKLFKSKMP
AVPEKVSVII DMDRLILTIF DGTEPVRQYP VAMGKYETPT PVGNWEIVSK SMNPPDAMGT
RWLGLNIPYG NYGIHGTNVP GSIGSFASHG CIRMHNAHVE EIFPSVTVGT AVTIVGTPFG
APGAPPSVLG LGSRGPDVLE VQRSLKRLGY LKWNPDGFWG EGTEKAVKKL RQDNGLKGMN
VVDDEVYNLL GL
//
