PBPD_BACSU
ID PBPD_BACSU Reviewed; 624 AA.
AC P40750; O05232;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 07-JUL-2009, sequence version 2.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=Penicillin-binding protein 4;
DE Short=PBP 4;
DE Includes:
DE RecName: Full=Penicillin-insensitive transglycosylase;
DE EC=2.4.1.129 {ECO:0000250|UniProtKB:P02918};
DE AltName: Full=Peptidoglycan TGase;
DE Includes:
DE RecName: Full=Penicillin-sensitive transpeptidase;
DE EC=3.4.16.4 {ECO:0000250|UniProtKB:P02918};
DE AltName: Full=DD-transpeptidase;
DE Flags: Precursor;
GN Name=pbpD {ECO:0000303|PubMed:7961491}; OrderedLocusNames=BSU31490;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 317-331, N-TERMINAL
RP BLOCKAGE, DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
RC STRAIN=168;
RX PubMed=7961491; DOI=10.1128/jb.176.23.7197-7205.1994;
RA Popham D.L., Setlow P.;
RT "Cloning, nucleotide sequence, mutagenesis, and mapping of the Bacillus
RT subtilis pbpD gene, which codes for penicillin-binding protein 4.";
RL J. Bacteriol. 176:7197-7205(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9274030; DOI=10.1099/00221287-143-8-2769;
RA Oudega B., Koningstein G., Rodrigues L., de Sales Ramon M., Hilbert H.,
RA Duesterhoeft A., Pohl T.M., Weitzenegger T.;
RT "Analysis of the Bacillus subtilis genome: cloning and nucleotide sequence
RT of a 62 kb region between 275 degrees (rrnB) and 284 degrees (pai).";
RL Microbiology 143:2769-2774(1997).
RN [3]
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 [4]
RP SEQUENCE REVISION TO 113-114.
RX PubMed=19383706; DOI=10.1099/mic.0.027839-0;
RA Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A.,
RA Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
RT "From a consortium sequence to a unified sequence: the Bacillus subtilis
RT 168 reference genome a decade later.";
RL Microbiology 155:1758-1775(2009).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=168 / PS832;
RX PubMed=9851991; DOI=10.1128/jb.180.24.6493-6502.1998;
RA Murray T., Popham D.L., Pearson C.B., Hand A.R., Setlow P.;
RT "Analysis of outgrowth of Bacillus subtilis spores lacking penicillin-
RT binding protein 2a.";
RL J. Bacteriol. 180:6493-6502(1998).
CC -!- FUNCTION: Cell wall formation. Synthesis of cross-linked peptidoglycan
CC from the lipid intermediates. The enzyme has a penicillin-insensitive
CC transglycosylase N-terminal domain (formation of linear glycan strands)
CC and a penicillin-sensitive transpeptidase C-terminal domain (cross-
CC linking of the peptide subunits) (Probable). Has a partially redundant
CC function with PBP-2A (pbpA) during spore outgrowth (PubMed:9851991).
CC {ECO:0000269|PubMed:9851991, ECO:0000305}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-
CC Ala)](n)-di-trans,octa-cis-undecaprenyl diphosphate + beta-D-GlcNAc-
CC (1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-
CC cis-undecaprenyl diphosphate = [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-
CC D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-di-trans-octa-cis-undecaprenyl
CC diphosphate + di-trans,octa-cis-undecaprenyl diphosphate + H(+);
CC Xref=Rhea:RHEA:23708, Rhea:RHEA-COMP:9602, Rhea:RHEA-COMP:9603,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:58405, ChEBI:CHEBI:60033,
CC ChEBI:CHEBI:78435; EC=2.4.1.129;
CC Evidence={ECO:0000250|UniProtKB:P02918};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Preferential cleavage: (Ac)2-L-Lys-D-Ala-|-D-Ala. Also
CC transpeptidation of peptidyl-alanyl moieties that are N-acyl
CC substituents of D-alanine.; EC=3.4.16.4;
CC Evidence={ECO:0000250|UniProtKB:P02918};
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Peripheral membrane
CC protein {ECO:0000305}.
CC -!- DEVELOPMENTAL STAGE: Expression increases during vegetative growth and
CC decreases soon after entry into sporulation.
CC {ECO:0000269|PubMed:7961491}.
CC -!- PTM: The N-terminus is blocked. {ECO:0000269|PubMed:7961491}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype (PubMed:7961491). Double
CC pbpA-pbpD deletions spores have greatly decreased spore outgrowth and
CC peptidoglycan synthesis (PubMed:9851991). {ECO:0000269|PubMed:7961491,
CC ECO:0000269|PubMed:9851991}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the
CC glycosyltransferase 51 family. {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the transpeptidase
CC family. {ECO:0000305}.
CC -!- CAUTION: It is uncertain whether Met-1 or Met-3 is the initiator.
CC {ECO:0000305}.
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DR EMBL; U11882; AAA64943.1; -; Genomic_DNA.
DR EMBL; Z93933; CAB07915.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB15138.2; -; Genomic_DNA.
DR PIR; A55220; A55220.
DR RefSeq; NP_391027.2; NC_000964.3.
DR RefSeq; WP_010886602.1; NZ_JNCM01000033.1.
DR AlphaFoldDB; P40750; -.
DR SMR; P40750; -.
DR IntAct; P40750; 1.
DR STRING; 224308.BSU31490; -.
DR BindingDB; P40750; -.
DR ChEMBL; CHEMBL3112382; -.
DR CAZy; GT51; Glycosyltransferase Family 51.
DR MEROPS; X52.001; -.
DR jPOST; P40750; -.
DR PaxDb; P40750; -.
DR PRIDE; P40750; -.
DR EnsemblBacteria; CAB15138; CAB15138; BSU_31490.
DR GeneID; 938851; -.
DR KEGG; bsu:BSU31490; -.
DR PATRIC; fig|224308.43.peg.3297; -.
DR eggNOG; COG0744; Bacteria.
DR InParanoid; P40750; -.
DR OMA; NDYHDMW; -.
DR PhylomeDB; P40750; -.
DR BioCyc; BSUB:BSU31490-MON; -.
DR PRO; PR:P40750; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0008658; F:penicillin binding; IBA:GO_Central.
DR GO; GO:0008955; F:peptidoglycan glycosyltransferase activity; IBA:GO_Central.
DR GO; GO:0009002; F:serine-type D-Ala-D-Ala carboxypeptidase activity; IEA:UniProtKB-EC.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IBA:GO_Central.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR GO; GO:0046677; P:response to antibiotic; IBA:GO_Central.
DR Gene3D; 1.10.3810.10; -; 1.
DR Gene3D; 3.40.710.10; -; 1.
DR InterPro; IPR012338; Beta-lactam/transpept-like.
DR InterPro; IPR001264; Glyco_trans_51.
DR InterPro; IPR023346; Lysozyme-like_dom_sf.
DR InterPro; IPR036950; PBP_transglycosylase.
DR InterPro; IPR001460; PCN-bd_Tpept.
DR Pfam; PF00912; Transgly; 1.
DR Pfam; PF00905; Transpeptidase; 1.
DR SUPFAM; SSF53955; SSF53955; 1.
DR SUPFAM; SSF56601; SSF56601; 1.
PE 1: Evidence at protein level;
KW Carboxypeptidase; Cell membrane; Cell shape;
KW Cell wall biogenesis/degradation; Direct protein sequencing;
KW Glycosyltransferase; Hydrolase; Membrane; Multifunctional enzyme;
KW Peptidoglycan synthesis; Protease; Reference proteome; Signal; Transferase.
FT SIGNAL 1..21
FT /evidence="ECO:0000255"
FT CHAIN 22..624
FT /note="Penicillin-binding protein 4"
FT /id="PRO_0000012147"
FT ACT_SITE 96
FT /note="Proton donor; for transglycosylase activity"
FT /evidence="ECO:0000250|UniProtKB:P02919"
FT ACT_SITE 388
FT /note="Acyl-ester intermediate; for transpeptidase
FT activity"
FT /evidence="ECO:0000250|UniProtKB:P02919"
FT CONFLICT 113..114
FT /note="RA -> PP (in Ref. 1; AAA64943 and 2; CAB07915)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 624 AA; 70659 MW; 6C41DD4B4EC7AB29 CRC64;
MTMLRKIIGW ILLLCIIPLF AFTVIASGKE VKQMKSLDQV LDKNIDLKDI SLVQNSYMYD
RDGSLVSEIV SDHENRVLVP FNKIPEEVKQ IFLTSEDRHF YEHKGFDFMG MVRATASNVK
DKKIDQGAST ITQQLSRNLY LSHERSFSRK LTELAYSYQL EKKYTKNEIL EAYLNTIYFN
NGVYGVGSAA QFYFSKPLKS LTVGEMAFIC AIPNNPTLYD PLKHFDYTKS RQERLLKGLK
DAGVITDKEL KKAVKQKIKL DVEKREDKYP DYVSYVNDEF TQLVSESEGF DKRLQKASGK
QKEKIENELS ARVSTLMKDG VKIYTALDPY MQNQVVAQMN SKLPYADVQG GAAVINHQTH
QIIALSGGKN YQKYDFNRAY QAYRQPGSSI KPLLDYGPYI EQTGATTSST IDASKFCSKD
YCPQNYNNRT YGTVTLDTAF KNSYNTPAIR MLDRVGIQKA FSYIEPYHFA KLVDSDYLLP
AALGGFTNGM TPLEMTKAYT TFGNSGSYTP SHAITKVTDL KGKTLYKWND KATQIFSVRT
NMQLKKLMSS VVKSGTGKKA YFNAPYIGGK TGTSNDYHDM WFVGLTDTYT MGVWVGKDTP
TSVEYLHSIS PQLSIWKGTL QAAY
