ID Q21GM9_SACD2 Unreviewed; 563 AA.
AC Q21GM9;
DT 18-APR-2006, integrated into UniProtKB/TrEMBL.
DT 18-APR-2006, sequence version 1.
DT 18-JUN-2025, entry version 99.
DE SubName: Full=Peptidoglycan-binding domain 1 {ECO:0000313|EMBL:ABD82150.1};
GN OrderedLocusNames=Sde_2893 {ECO:0000313|EMBL:ABD82150.1};
OS Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024).
OC Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC Cellvibrionales; Cellvibrionaceae; Saccharophagus.
OX NCBI_TaxID=203122 {ECO:0000313|EMBL:ABD82150.1, ECO:0000313|Proteomes:UP000001947};
RN [1] {ECO:0000313|EMBL:ABD82150.1, ECO:0000313|Proteomes:UP000001947}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=2-40 / ATCC 43961 / DSM 17024
RC {ECO:0000313|Proteomes:UP000001947};
RX PubMed=18516288; DOI=10.1371/journal.pgen.1000087;
RA Weiner R.M., Taylor L.E.II., Henrissat B., Hauser L., Land M.,
RA Coutinho P.M., Rancurel C., Saunders E.H., Longmire A.G., Zhang H.,
RA Bayer E.A., Gilbert H.J., Larimer F., Zhulin I.B., Ekborg N.A., Lamed R.,
RA Richardson P.M., Borovok I., Hutcheson S.;
RT "Complete genome sequence of the complex carbohydrate-degrading marine
RT bacterium, Saccharophagus degradans strain 2-40 T.";
RL PLoS Genet. 4:E1000087-E1000087(2008).
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}.
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DR EMBL; CP000282; ABD82150.1; -; Genomic_DNA.
DR RefSeq; WP_011469366.1; NC_007912.1.
DR AlphaFoldDB; Q21GM9; -.
DR STRING; 203122.Sde_2893; -.
DR GeneID; 98614537; -.
DR KEGG; sde:Sde_2893; -.
DR eggNOG; COG2989; Bacteria.
DR HOGENOM; CLU_020360_3_4_6; -.
DR OrthoDB; 9778545at2; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000001947; Chromosome.
DR GO; GO:0004180; F:carboxypeptidase activity; IEA:UniProtKB-ARBA.
DR GO; GO:0016740; F:transferase activity; IEA:UniProtKB-KW.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-UniRule.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniPathway.
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; 1.
DR InterPro; IPR052905; LD-transpeptidase_YkuD-like.
DR InterPro; IPR005490; LD_TPept_cat_dom.
DR InterPro; IPR045380; LD_TPept_scaffold_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; PTHR41533:SF2; BLR7131 PROTEIN; 1.
DR PANTHER; PTHR41533; L,D-TRANSPEPTIDASE HI_1667-RELATED; 1.
DR Pfam; PF01471; PG_binding_1; 1.
DR Pfam; PF20142; Scaffold; 1.
DR Pfam; PF03734; YkuD; 1.
DR SUPFAM; SSF141523; L,D-transpeptidase catalytic domain-like; 1.
DR SUPFAM; SSF47090; PGBD-like; 1.
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 Peptidoglycan synthesis {ECO:0000256|ARBA:ARBA00022984,
KW ECO:0000256|PROSITE-ProRule:PRU01373};
KW Reference proteome {ECO:0000313|Proteomes:UP000001947};
KW Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT DOMAIN 331..506
FT /note="L,D-TPase catalytic"
FT /evidence="ECO:0000259|PROSITE:PS52029"
FT ACT_SITE 463
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01373"
FT ACT_SITE 482
FT /note="Nucleophile"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU01373"
SQ SEQUENCE 563 AA; 63453 MW; A477B57BCF4BDD96 CRC64;
MYFNGSLFFT LSFFSHHRLS HYIHAFRRDL VAVICALVLA GDAFASSALQ GAAVNDSIRQ
RLEAWSAGYP AKISSAPIRN SALLNAYYEE TGFAPLWLKD SGRAFNSAAL DLIAVLQGVD
KEGLLPADYH IAYLGQLITE PSEISSDAEL VLTDAFLFLA QHILAGKVDP ETLTNEWKPA
KEVVDARALL TKVASNVPIA DIVQSLRPRQ PRYARLVKTL AWLNSTQAPD WEPLALSPAI
KKGMADTRLS PIAERLRFWG DLSESEETFT HYEGELMEAV TRFQRRHGLE PDGVVGKNTL
LALNVSPVQR ANDVVVNLER WRWLDQNMGD YFIVVNIANF DLRVYKSNEL VMQKPVIVGR
NYRKTPVFSD KIRFLVFNPT WTVPQKLAVQ DKLPEIKKDI SYLEKYGFTL YALGENTVVN
PADVEWDKLH KRFPYRMVQA PGPLNALGQV KFMFPNAYDV YLHDTPSREL FSKTERAFSS
GCIRVSDPIE LASKLLEPNG MGIDQINEVL SSAKTTTVNL KTPVPVHIEY WTAWVDSSGK
LQFRNDIYER DKPLFSALTL PIE
//
