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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)DescriptionActionsGraphical viewLength
Active sitei60Acyl-ester intermediateBy similarity1
Active sitei63Proton acceptorBy similarity1
Active sitei115By similarity1
Binding sitei220SubstrateBy similarity1

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)DescriptionActionsGraphical viewLength
Signal peptidei1 – 271 PublicationAdd BLAST27
ChainiPRO_000002722928 – 382D-alanyl-D-alanine carboxypeptidase DacBAdd BLAST355

Proteomic databases

PaxDbiP35150.
PRIDEiP35150.

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

1382
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi34 – 40Combined sources7
Turni41 – 43Combined sources3
Beta strandi46 – 51Combined sources6
Helixi59 – 62Combined sources4
Helixi63 – 72Combined sources10
Beta strandi78 – 81Combined sources4
Helixi84 – 88Combined sources5
Beta strandi101 – 103Combined sources3
Helixi104 – 114Combined sources11
Helixi117 – 128Combined sources12
Helixi131 – 145Combined sources15
Beta strandi153 – 156Combined sources4
Beta strandi161 – 163Combined sources3
Helixi168 – 178Combined sources11
Helixi182 – 188Combined sources7
Beta strandi191 – 194Combined sources4
Beta strandi196 – 199Combined sources4
Beta strandi201 – 203Combined sources3
Helixi207 – 210Combined sources4
Beta strandi216 – 224Combined sources9
Turni225 – 227Combined sources3
Beta strandi228 – 237Combined sources10
Beta strandi240 – 248Combined sources9
Helixi252 – 266Combined sources15
Beta strandi267 – 273Combined sources7
Beta strandi275 – 277Combined sources3
Helixi279 – 281Combined sources3
Turni285 – 289Combined sources5
Beta strandi290 – 294Combined sources5
Beta strandi296 – 301Combined sources6
Helixi302 – 305Combined sources4
Beta strandi308 – 314Combined sources7
Helixi320 – 323Combined sources4
Helixi325 – 327Combined sources3
Beta strandi330 – 339Combined sources10
Beta strandi342 – 351Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3MFDX-ray1.75A/B27-358[»]
ProteinModelPortaliP35150.
SMRiP35150.
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.
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)DescriptionActionsGraphical viewLength
Sequence conflicti179 – 194MKLKD…TKIYK → IEAERLSKDFRHKNIQ AA sequence (PubMed:1548223).CuratedAdd BLAST16

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3MFDX-ray1.75A/B27-358[»]
ProteinModelPortaliP35150.
SMRiP35150.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100012736.

Protein family/group databases

MEROPSiS11.004.

Proteomic databases

PaxDbiP35150.
PRIDEiP35150.

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.
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...

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: November 2, 2016
This is version 129 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.