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UniProtKB - O34798 (PDAC_BACSU)
Protein
Peptidoglycan-N-acetylmuramic acid deacetylase PdaC
Gene
pdaC
Organism
Bacillus subtilis (strain 168)
Status
Functioni
Catalyzes the deacetylation of N-acetylmuramic acid (MurNAc) residues in peptidoglycan, a modification that confers resistance to lysosyme. Is not able to deacetylate N-acetylglucosamine (GlcNAc) residues in peptidoglycan, but can deacylate chitin oligomers such as GlcNAc4 and GlcNAc5. Is essentially not active toward chitosan (partially deacetylated GlcNAc polymer) and has very low activity toward chitin (GlcNAc polymer). Does not deacetylate GlcNAc.
1 PublicationMiscellaneous
The product of deacetylated GlcNAc4 by PdaC is GlcNAc-GlcNAc-GlcN-GlcNAc.1 Publication
Derepression of pdaC in cells depleted for yycFG leads to increased resistance of the cell walls to lysozyme digestion.
Caution
Was originally described as a deoxyribonuclease (PubMed:17878218), but it was later shown that PdaC has no DNase activity at all (PubMed:22277649).2 Publications
Activity regulationi
Activated by divalent metal cations; Mn2+ is the most efficient, followed by Ca2+ and Mg2+. In contrast to PgdA from S.pneumoniae, these ions are not absolutely required for deacetylase activity.1 Publication
Kineticsi
kcat is 0.32 sec(-1) for the deacetylation of MurNAc residues in peptidoglycan, and 0.24 sec(-1) for the deacetylation of GlcNAc4.
- KM=4.8 mM for non-treated B.subtilis peptidoglycan1 Publication
- KM=12.3 mM for GlcNAc41 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 285 | Proton acceptorBy similarity | 1 | |
Metal bindingi | 286 | Divalent metal cationBy similarity | 1 | |
Metal bindingi | 336 | Divalent metal cation; via tele nitrogenBy similarity | 1 | |
Metal bindingi | 340 | Divalent metal cation; via tele nitrogenBy similarity | 1 | |
Sitei | 401 | Raises pKa of active site HisBy similarity | 1 | |
Active sitei | 427 | Proton donorBy similarity | 1 |
GO - Molecular functioni
- hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Source: InterPro
- metal ion binding Source: UniProtKB-KW
GO - Biological processi
- carbohydrate metabolic process Source: InterPro
Keywordsi
Molecular function | Hydrolase |
Ligand | Metal-binding |
Enzyme and pathway databases
BioCyci | BSUB:BSU12100-MONOMER |
Names & Taxonomyi
Protein namesi | Recommended name: Peptidoglycan-N-acetylmuramic acid deacetylase PdaC (EC:3.5.1.-)Short name: Peptidoglycan MurNAc deacetylase Alternative name(s): Polysaccharide deacetylase PdaC |
Gene namesi | Name:pdaC Synonyms:yjeA Ordered Locus Names:BSU12100 |
Organismi | Bacillus subtilis (strain 168) |
Taxonomic identifieri | 224308 [NCBI] |
Taxonomic lineagei | Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus › |
Proteomesi |
|
Subcellular locationi
Plasma membrane
- Cell membrane Curated; Single-pass membrane protein Curated
Plasma Membrane
- plasma membrane Source: UniProtKB-SubCell
Other locations
- integral component of membrane Source: UniProtKB-KW
Topology
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Transmembranei | 6 – 26 | HelicalSequence analysisAdd BLAST | 21 |
Keywords - Cellular componenti
Cell membrane, MembranePathology & Biotechi
Disruption phenotypei
Cells lacking this gene show sensitivity to lysosyme, in contrast to wild-type.1 Publication
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000024846 | 1 – 467 | Peptidoglycan-N-acetylmuramic acid deacetylase PdaCAdd BLAST | 467 |
Proteomic databases
PaxDbi | O34798 |
Expressioni
Inductioni
Negatively regulated by the two-component system YycFG.1 Publication
Interactioni
Protein-protein interaction databases
IntActi | O34798, 2 interactors |
STRINGi | 224308.BSU12100 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | O34798 |
ModBasei | Search... |
PDBe-KBi | Search... |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 278 – 452 | NodB homologyPROSITE-ProRule annotationAdd BLAST | 175 |
Sequence similaritiesi
In the N-terminal section; belongs to the RsiV family.Curated
In the C-terminal section; belongs to the polysaccharide deacetylase family.Curated
Keywords - Domaini
Transmembrane, Transmembrane helixPhylogenomic databases
eggNOGi | COG0726, Bacteria |
OMAi | VQYYPET |
Family and domain databases
Gene3Di | 3.90.640.20, 1 hit |
InterProi | View protein in InterPro IPR021729, DUF3298 IPR011330, Glyco_hydro/deAcase_b/a-brl IPR002509, NODB_dom IPR025303, PdaC IPR037126, PdaC/RsiV-like_sf IPR017219, Peptidoglycan_deacetylase |
Pfami | View protein in Pfam PF11738, DUF3298, 1 hit PF13739, PdaC, 1 hit PF01522, Polysacc_deac_1, 1 hit |
PIRSFi | PIRSF037479, PG_GlcNAc_deacetylase, 1 hit |
SUPFAMi | SSF88713, SSF88713, 1 hit |
PROSITEi | View protein in PROSITE PS51677, NODB, 1 hit |
i Sequence
Sequence statusi: Complete.
O34798-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MLAKRIKWFH VLIAVVCVVG LIGFFHNHSL KKETVMNKVR TDSQYGNVEI
60 70 80 90 100
ATLVNDGKTF NYAVNYPVFK NEKMDSALKR FAEKEVRQFQ KETKDVDQEH
110 120 130 140 150
TTKRNELNVD YKIVHYAKQT VAIVFNEYKY IGGAHGQTVK KTFNYDFSKQ
160 170 180 190 200
AFLSIDDIFK EDADYLHKLS LIAYHELKKN KDIAADDALL KEGTAPKKEN
210 220 230 240 250
FSRFAIKEDY IELYFDTYQV AAGYLGEQSI AIKKSLLKDI LKEQYIDKAK
260 270 280 290 300
NKNKIKEQKP KHEVISLPKE ETVDPNQKVI ALTFDDGPNP ATTNQILDSL
310 320 330 340 350
KKYKGHATFF VLGSRVQYYP ETLIRMLKEG NEVGNHSWSH PLLTRLSVKE
360 370 380 390 400
ALKQINDTQD IIEKISGYRP TLVRPPYGGI NDELRSQMKM DVALWDVDPE
410 420 430 440 450
DWKDRNKKTI VDRVMNQAGD GRTILIHDIY RTSADAADEI IKKLTDQGYQ
460
LVTVSQLEEV KKQREAK
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF015825 Genomic DNA Translation: AAC46306.1 AL009126 Genomic DNA Translation: CAB13067.1 |
PIRi | G69849 |
RefSeqi | NP_389092.1, NC_000964.3 WP_003245023.1, NZ_JNCM01000035.1 |
Genome annotation databases
EnsemblBacteriai | CAB13067; CAB13067; BSU_12100 |
GeneIDi | 936440 |
KEGGi | bsu:BSU12100 |
PATRICi | fig|224308.179.peg.1307 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF015825 Genomic DNA Translation: AAC46306.1 AL009126 Genomic DNA Translation: CAB13067.1 |
PIRi | G69849 |
RefSeqi | NP_389092.1, NC_000964.3 WP_003245023.1, NZ_JNCM01000035.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
6H8L | X-ray | 1.54 | A/B | 270-467 | [»] | |
6H8N | X-ray | 1.26 | A/B | 270-467 | [»] | |
SMRi | O34798 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
IntActi | O34798, 2 interactors |
STRINGi | 224308.BSU12100 |
Proteomic databases
PaxDbi | O34798 |
Genome annotation databases
EnsemblBacteriai | CAB13067; CAB13067; BSU_12100 |
GeneIDi | 936440 |
KEGGi | bsu:BSU12100 |
PATRICi | fig|224308.179.peg.1307 |
Phylogenomic databases
eggNOGi | COG0726, Bacteria |
OMAi | VQYYPET |
Enzyme and pathway databases
BioCyci | BSUB:BSU12100-MONOMER |
Family and domain databases
Gene3Di | 3.90.640.20, 1 hit |
InterProi | View protein in InterPro IPR021729, DUF3298 IPR011330, Glyco_hydro/deAcase_b/a-brl IPR002509, NODB_dom IPR025303, PdaC IPR037126, PdaC/RsiV-like_sf IPR017219, Peptidoglycan_deacetylase |
Pfami | View protein in Pfam PF11738, DUF3298, 1 hit PF13739, PdaC, 1 hit PF01522, Polysacc_deac_1, 1 hit |
PIRSFi | PIRSF037479, PG_GlcNAc_deacetylase, 1 hit |
SUPFAMi | SSF88713, SSF88713, 1 hit |
PROSITEi | View protein in PROSITE PS51677, NODB, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | PDAC_BACSU | |
Accessioni | O34798Primary (citable) accession number: O34798 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | November 25, 2002 |
Last sequence update: | January 1, 1998 | |
Last modified: | February 23, 2022 | |
This is version 118 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families