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Protein

D-alanyl-D-alanine carboxypeptidase DacB

Gene

dacB

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors. Required specifically for the synthesis of the spore form of peptidoglycan (cortex).

Catalytic activityi

Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.

Pathwayi: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei60 – 601Acyl-ester intermediateBy similarity
Active sitei63 – 631Proton acceptorBy similarity
Active sitei115 – 1151By similarity
Binding sitei220 – 2201SubstrateBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Carboxypeptidase, Hydrolase, Protease

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis, Sporulation

Enzyme and pathway databases

BioCyciBSUB:BSU23190-MONOMER.
UniPathwayiUPA00219.

Protein family/group databases

MEROPSiS11.004.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanyl-D-alanine carboxypeptidase DacB (EC:3.4.16.4)
Short name:
DD-carboxypeptidase
Short name:
DD-peptidase
Alternative name(s):
Penicillin-binding protein 5*
Short name:
PBP-5*
Gene namesi
Name:dacB
Ordered Locus Names:BSU23190
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 27271 PublicationAdd
BLAST
Chaini28 – 382355D-alanyl-D-alanine carboxypeptidase DacBPRO_0000027229Add
BLAST

Proteomic databases

PaxDbiP35150.

Expressioni

Developmental stagei

Expressed at about stage III of sporulation. Likely to be expressed specifically in the mother cell.

Interactioni

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100012736.

Structurei

Secondary structure

1
382
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi34 – 407Combined sources
Turni41 – 433Combined sources
Beta strandi46 – 516Combined sources
Helixi59 – 624Combined sources
Helixi63 – 7210Combined sources
Beta strandi78 – 814Combined sources
Helixi84 – 885Combined sources
Beta strandi101 – 1033Combined sources
Helixi104 – 11411Combined sources
Helixi117 – 12812Combined sources
Helixi131 – 14515Combined sources
Beta strandi153 – 1564Combined sources
Beta strandi161 – 1633Combined sources
Helixi168 – 17811Combined sources
Helixi182 – 1887Combined sources
Beta strandi191 – 1944Combined sources
Beta strandi196 – 1994Combined sources
Beta strandi201 – 2033Combined sources
Helixi207 – 2104Combined sources
Beta strandi216 – 2249Combined sources
Turni225 – 2273Combined sources
Beta strandi228 – 23710Combined sources
Beta strandi240 – 2489Combined sources
Helixi252 – 26615Combined sources
Beta strandi267 – 2737Combined sources
Beta strandi275 – 2773Combined sources
Helixi279 – 2813Combined sources
Turni285 – 2895Combined sources
Beta strandi290 – 2945Combined sources
Beta strandi296 – 3016Combined sources
Helixi302 – 3054Combined sources
Beta strandi308 – 3147Combined sources
Helixi320 – 3234Combined sources
Helixi325 – 3273Combined sources
Beta strandi330 – 33910Combined sources
Beta strandi342 – 35110Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3MFDX-ray1.75A/B27-358[»]
ProteinModelPortaliP35150.
SMRiP35150. Positions 28-353.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP35150.

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase S11 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105DZ1. Bacteria.
COG1686. LUCA.
HOGENOMiHOG000086625.
InParanoidiP35150.
KOiK01286.
OMAiVPGSSMY.
OrthoDBiEOG6RJV2H.
PhylomeDBiP35150.

Family and domain databases

Gene3Di3.40.710.10. 1 hit.
InterProiIPR012338. Beta-lactam/transpept-like.
IPR018044. Peptidase_S11.
IPR012907. Peptidase_S11_C.
IPR001967. Peptidase_S11_N.
[Graphical view]
PfamiPF07943. PBP5_C. 1 hit.
PF00768. Peptidase_S11. 1 hit.
[Graphical view]
PRINTSiPR00725. DADACBPTASE1.
SMARTiSM00936. PBP5_C. 1 hit.
[Graphical view]
SUPFAMiSSF56601. SSF56601. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P35150-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRIFKKAVFV IMISFLIATV NVNTAHAAID VSAKSAIIID GASGRVLYAK
60 70 80 90 100
DEHQKRRIAS ITKIMTAVLA IESGKMDQTV TVSANAVRTE GSAIYLTEGQ
110 120 130 140 150
KVKLKDLVYG LMLRSGNDAA VAIAEHVGGS LDGFVYMMNQ KAEQLGMKNT
160 170 180 190 200
RFQNPHGLDD HENHYSTAYD MAILTKYAMK LKDYQKISGT KIYKAETMES
210 220 230 240 250
VWKNKNKLLT MLYPYSTGGK TGYTKLAKRT LVSTASKDGI DLIAVTINDP
260 270 280 290 300
NDWDDHMKMF NYVFEHYQTY LIAKKGDIPK LKGTFYESKA FIKRDITYLL
310 320 330 340 350
TEEEKENVKI NTTLLKPKKA WEKDASKIPD IVGHMEIMFN DATIAKVPIY
360 370 380
YENERHQKPK KQFFETFKSI FLNAAGGAKW SI
Length:382
Mass (Da):43,081
Last modified:February 1, 1994 - v1
Checksum:i484D89F785A092DB
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti179 – 19416MKLKD…TKIYK → IEAERLSKDFRHKNIQ AA sequence (PubMed:1548223).CuratedAdd
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M84227 Genomic DNA. Translation: AAA22377.1.
L09228 Genomic DNA. Translation: AAA67490.1.
AL009126 Genomic DNA. Translation: CAB14251.1.
PIRiS45552.
RefSeqiNP_390200.1. NC_000964.3.
WP_003230505.1. NZ_JNCM01000036.1.

Genome annotation databases

EnsemblBacteriaiCAB14251; CAB14251; BSU23190.
GeneIDi938953.
KEGGibsu:BSU23190.
PATRICi18976455. VBIBacSub10457_2418.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M84227 Genomic DNA. Translation: AAA22377.1.
L09228 Genomic DNA. Translation: AAA67490.1.
AL009126 Genomic DNA. Translation: CAB14251.1.
PIRiS45552.
RefSeqiNP_390200.1. NC_000964.3.
WP_003230505.1. NZ_JNCM01000036.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3MFDX-ray1.75A/B27-358[»]
ProteinModelPortaliP35150.
SMRiP35150. Positions 28-353.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100012736.

Protein family/group databases

MEROPSiS11.004.

Proteomic databases

PaxDbiP35150.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB14251; CAB14251; BSU23190.
GeneIDi938953.
KEGGibsu:BSU23190.
PATRICi18976455. VBIBacSub10457_2418.

Phylogenomic databases

eggNOGiENOG4105DZ1. Bacteria.
COG1686. LUCA.
HOGENOMiHOG000086625.
InParanoidiP35150.
KOiK01286.
OMAiVPGSSMY.
OrthoDBiEOG6RJV2H.
PhylomeDBiP35150.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciBSUB:BSU23190-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP35150.

Family and domain databases

Gene3Di3.40.710.10. 1 hit.
InterProiIPR012338. Beta-lactam/transpept-like.
IPR018044. Peptidase_S11.
IPR012907. Peptidase_S11_C.
IPR001967. Peptidase_S11_N.
[Graphical view]
PfamiPF07943. PBP5_C. 1 hit.
PF00768. Peptidase_S11. 1 hit.
[Graphical view]
PRINTSiPR00725. DADACBPTASE1.
SMARTiSM00936. PBP5_C. 1 hit.
[Graphical view]
SUPFAMiSSF56601. SSF56601. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation and sequence analysis of dacB, which encodes a sporulation-specific penicillin-binding protein in Bacillus subtilis."
    Buchanan C.E., Ling M.-L.
    J. Bacteriol. 174:1717-1725(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 28-44.
  2. "The organization of the Bacillus subtilis 168 chromosome region between the spoVA and serA genetic loci, based on sequence data."
    Sorokin A.V., Zumstein E., Azevedo V., Ehrlich S.D., Serror P.
    Mol. Microbiol. 10:385-395(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
  3. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.

Entry informationi

Entry nameiDACB_BACSU
AccessioniPrimary (citable) accession number: P35150
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: June 8, 2016
This is version 126 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. Peptidase families
    Classification of peptidase families and list of entries
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.