YCBB_ECOLI
ID YCBB_ECOLI Reviewed; 615 AA.
AC P22525; P75847;
DT 01-AUG-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 165.
DE RecName: Full=Probable L,D-transpeptidase YcbB;
DE EC=2.-.-.-;
GN Name=ycbB; OrderedLocusNames=b0925, JW0908;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-63.
RX PubMed=1989883; DOI=10.1002/j.1460-2075.1991.tb07935.x;
RA Niki H., Jaffe A., Imamura R., Ogura T., Hiraga S.;
RT "The new gene mukB codes for a 177 kd protein with coiled-coil domains
RT involved in chromosome partitioning of E. coli.";
RL EMBO J. 10:183-193(1991).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / BW25113;
RX PubMed=18456808; DOI=10.1128/jb.00025-08;
RA Magnet S., Dubost L., Marie A., Arthur M., Gutmann L.;
RT "Identification of the L,D-transpeptidases for peptidoglycan cross-linking
RT in Escherichia coli.";
RL J. Bacteriol. 190:4782-4785(2008).
CC -!- FUNCTION: Responsible, at least in part, for generating a meso-
CC diaminopimelyl-3-a meso-diaminopimelyl-3 cross-link.
CC {ECO:0000269|PubMed:18456808}.
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000305}; Single-pass membrane
CC protein {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Simultaneous disruption of erfK, ybiS, ycfS and
CC ynhG leads to loss of a significant proportion of muropeptides,
CC including those with meso-DAP-3-meso-DAP-3 cross-links and with
CC covalently anchored major outer membrane lipoprotein (Lpp) to the
CC peptidoglycan. Overexpression of ycbB in this background increases
CC meso-diaminopimelyl-3-a meso-diaminopimelyl-3 cross-links but does not
CC restore Lpp anchoring. {ECO:0000269|PubMed:18456808}.
CC -!- SIMILARITY: Belongs to the YkuD family. {ECO:0000305}.
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DR EMBL; U00096; AAC74011.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35671.1; -; Genomic_DNA.
DR EMBL; X57550; CAA40777.1; -; Genomic_DNA.
DR PIR; D64832; D64832.
DR RefSeq; NP_415445.1; NC_000913.3.
DR RefSeq; WP_000925969.1; NZ_LN832404.1.
DR PDB; 6NTW; X-ray; 2.76 A; A=31-615.
DR PDBsum; 6NTW; -.
DR AlphaFoldDB; P22525; -.
DR SMR; P22525; -.
DR BioGRID; 4260015; 128.
DR DIP; DIP-11474N; -.
DR IntAct; P22525; 8.
DR STRING; 511145.b0925; -.
DR jPOST; P22525; -.
DR PaxDb; P22525; -.
DR PRIDE; P22525; -.
DR EnsemblBacteria; AAC74011; AAC74011; b0925.
DR EnsemblBacteria; BAA35671; BAA35671; BAA35671.
DR GeneID; 945541; -.
DR KEGG; ecj:JW0908; -.
DR KEGG; eco:b0925; -.
DR PATRIC; fig|511145.12.peg.956; -.
DR EchoBASE; EB1233; -.
DR eggNOG; COG2989; Bacteria.
DR HOGENOM; CLU_020360_3_0_6; -.
DR InParanoid; P22525; -.
DR OMA; HNLFQRD; -.
DR PhylomeDB; P22525; -.
DR BioCyc; EcoCyc:EG11253-MON; -.
DR BioCyc; MetaCyc:EG11253-MON; -.
DR BRENDA; 2.3.2.B14; 2026.
DR UniPathway; UPA00219; -.
DR PRO; PR:P22525; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0004180; F:carboxypeptidase activity; IDA:EcoCyc.
DR GO; GO:0016807; F:cysteine-type carboxypeptidase activity; ISM:EcoCyc.
DR GO; GO:0016757; F:glycosyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0071972; F:peptidoglycan L,D-transpeptidase activity; IDA:EcoCyc.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0036460; P:cellular response to cell envelope stress; IDA:EcoCyc.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IEP:EcoliWiki.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IDA:EcoCyc.
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:0046677; P:response to antibiotic; IDA:EcoCyc.
DR CDD; cd16913; YkuD_like; 1.
DR Gene3D; 1.10.101.10; -; 1.
DR Gene3D; 2.40.440.10; -; 1.
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 Pfam; PF01471; PG_binding_1; 1.
DR Pfam; PF20142; Scaffold; 1.
DR Pfam; PF03734; YkuD; 1.
DR SUPFAM; SSF141523; SSF141523; 1.
DR SUPFAM; SSF47090; SSF47090; 1.
DR PROSITE; PS00092; N6_MTASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell shape; Cell wall biogenesis/degradation;
KW Glycosyltransferase; Hydrolase; Membrane; Peptidoglycan synthesis;
KW Reference proteome; Transferase; Transmembrane; Transmembrane helix.
FT CHAIN 1..615
FT /note="Probable L,D-transpeptidase YcbB"
FT /id="PRO_0000168766"
FT TRANSMEM 11..26
FT /note="Helical"
FT /evidence="ECO:0000255"
FT REGION 288..312
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 288..309
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 528
FT /evidence="ECO:0000255"
FT CONFLICT 39..40
FT /note="DS -> ER (in Ref. 4; CAA40777)"
FT /evidence="ECO:0000305"
FT HELIX 41..46
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 78..81
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 91..100
FT /evidence="ECO:0007829|PDB:6NTW"
FT TURN 101..103
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 110..126
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 131..139
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 147..174
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 188..199
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 203..208
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 217..229
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 252..261
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 319..331
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 342..349
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 352..365
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 366..368
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 375..380
FT /evidence="ECO:0007829|PDB:6NTW"
FT TURN 381..384
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 385..390
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 393..403
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 405..407
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 412..415
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 418..422
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 429..435
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 437..440
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 445..449
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 452..456
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 466..468
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 471..473
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 482..485
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 491..493
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 495..499
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 502..505
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 514..518
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 523..527
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 529..531
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 534..543
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 544..546
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 549..558
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 562..565
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 571..575
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 578..581
FT /evidence="ECO:0007829|PDB:6NTW"
FT STRAND 585..589
FT /evidence="ECO:0007829|PDB:6NTW"
FT HELIX 606..613
FT /evidence="ECO:0007829|PDB:6NTW"
SQ SEQUENCE 615 AA; 67812 MW; CB16D78CFFD70C57 CRC64;
MLLNMMCGRQ LSAISLCLAV TFAPLFNAQA DEPEVIPGDS PVAVSEQGEA LPQAQATAIM
AGIQPLPEGA AEKARTQIES QLPAGYKPVY LNQLQLLYAA RDMQPMWENR DAVKAFQQQL
AEVAIAGFQP QFNKWVELLT DPGVNGMARD VVLSDAMMGY LHFIANIPVK GTRWLYSSKP
YALATPPLSV INQWQLALDK GQLPTFVAGL APQHPQYAAM HESLLALLCD TKPWPQLTGK
ATLRPGQWSN DVPALREILQ RTGMLDGGPK ITLPGDDTPT DAVVSPSAVT VETAETKPMD
KQTTSRSKPA PAVRAAYDNE LVEAVKRFQA WQGLGADGAI GPATRDWLNV TPAQRAGVLA
LNIQRLRLLP TELSTGIMVN IPAYSLVYYQ NGNQVLDSRV IVGRPDRKTP MMSSALNNVV
VNPPWNVPPT LARKDILPKV RNDPGYLESH GYTVMRGWNS REAIDPWQVD WSTITASNLP
FRFQQAPGPR NSLGRYKFNM PSSEAIYLHD TPNHNLFKRD TRALSSGCVR VNKASDLANM
LLQDAGWNDK RISDALKQGD TRYVNIRQSI PVNLYYLTAF VGADGRTQYR TDIYNYDLPA
RSSSQIVSKA EQLIR
