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Protein

Peptidoglycan-N-acetylmuramic acid deacetylase PdaA

Gene

pdaA

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

Functioni

Catalyzes the deacetylation of N-acetylmuramic acid (MurNAc) residues in glycan strands of peptidoglycan, leading to the formation of muramic delta-lactam residues in spore cortex, after transpeptidation of deacetylated muramic acid residues. PdaA probably carries out both deacetylation and lactam ring formation and requires the product of CwlD activity on peptidoglycan as a substrate. Is required for germination. Cannot use chitin oligomer (hexa-N-acetylchitohexaose) as a substrate.3 Publications

Miscellaneous

CwlD and PdaA are necessary and sufficient for muramic delta-lactam production in B.subtilis spore peptidoglycan.1 Publication

pH dependencei

Optimum pH is 7.0.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei73Proton acceptorBy similarity1
Metal bindingi124Divalent metal cation; via tele nitrogen1
Metal bindingi128Divalent metal cation; via tele nitrogen1
Sitei193Raises pKa of active site HisBy similarity1
Active sitei222Proton donorBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase
Biological processCell wall biogenesis/degradation, Sporulation
LigandMetal-binding

Enzyme and pathway databases

BioCyciBSUB:BSU07980-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
Peptidoglycan-N-acetylmuramic acid deacetylase PdaA (EC:3.5.1.-)
Short name:
Peptidoglycan MurNAc deacetylase
Gene namesi
Name:pdaA
Synonyms:yfjS
Ordered Locus Names:BSU07980
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Pathology & Biotechi

Disruption phenotypei

Spores have no muramic delta-lactam structure in the cortex and cannot germinate. Mutant spore peptidoglycan possesses many MurNAc residues lacking peptide side chains.2 Publications

Chemistry databases

DrugBankiDB03740 N-acetyl-alpha-D-glucosamine

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 23Sequence analysisAdd BLAST23
ChainiPRO_000002484224 – 263Peptidoglycan-N-acetylmuramic acid deacetylase PdaAAdd BLAST240

Proteomic databases

PaxDbiO34928
PRIDEiO34928

Expressioni

Developmental stagei

Expressed in the forespore, then exported into the developing cortex.1 Publication

Inductioni

Expression is sigma G-dependent.1 Publication

Interactioni

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100004443

Structurei

Secondary structure

1263
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi46 – 54Combined sources9
Beta strandi58 – 60Combined sources3
Beta strandi65 – 76Combined sources12
Helixi81 – 90Combined sources10
Beta strandi96 – 99Combined sources4
Helixi101 – 106Combined sources6
Helixi108 – 116Combined sources9
Beta strandi120 – 123Combined sources4
Helixi131 – 133Combined sources3
Helixi136 – 154Combined sources19
Helixi165 – 167Combined sources3
Helixi171 – 179Combined sources9
Beta strandi183 – 185Combined sources3
Helixi196 – 198Combined sources3
Helixi202 – 211Combined sources10
Beta strandi217 – 221Combined sources5
Helixi228 – 242Combined sources15
Beta strandi245 – 247Combined sources3
Helixi249 – 257Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NY1X-ray1.80A/B24-263[»]
1W17X-ray1.90A/B1-263[»]
1W1AX-ray2.251/212-263[»]
1W1BX-ray2.101/212-263[»]
ProteinModelPortaliO34928
SMRiO34928
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO34928

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini66 – 247NodB homologyPROSITE-ProRule annotationAdd BLAST182

Sequence similaritiesi

Belongs to the polysaccharide deacetylase family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiCOG0726 LUCA
HOGENOMiHOG000260720
InParanoidiO34928
KOiK01567
OMAiHDRRSWT
PhylomeDBiO34928

Family and domain databases

CDDicd10948 CE4_BsPdaA_like, 1 hit
InterProiView protein in InterPro
IPR011330 Glyco_hydro/deAcase_b/a-brl
IPR002509 NODB_dom
IPR014235 Spore_PdaA
PANTHERiPTHR10587:SF78 PTHR10587:SF78, 1 hit
PfamiView protein in Pfam
PF01522 Polysacc_deac_1, 1 hit
SUPFAMiSSF88713 SSF88713, 1 hit
TIGRFAMsiTIGR02884 spore_pdaA, 1 hit
PROSITEiView protein in PROSITE
PS51677 NODB, 1 hit

Sequencei

Sequence statusi: Complete.

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

O34928-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKWMCSICCA AVLLAGGAAQ AEAVPNEPIN WGFKRSVNHQ PPDAGKQLNS
60 70 80 90 100
LIEKYDAFYL GNTKEKTIYL TFDNGYENGY TPKVLDVLKK HRVTGTFFVT
110 120 130 140 150
GHFVKDQPQL IKRMSDEGHI IGNHSFHHPD LTTKTADQIQ DELDSVNEEV
160 170 180 190 200
YKITGKQDNL YLRPPRGVFS EYVLKETKRL GYQTVFWSVA FVDWKINNQK
210 220 230 240 250
GKKYAYDHMI KQAHPGAIYL LHTVSRDNAE ALDDAITDLK KQGYTFKSID
260
DLMFEKEMRL PSL
Length:263
Mass (Da):30,069
Last modified:January 1, 1998 - v1
Checksum:iFEA2251646D169A0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D83967 Genomic DNA Translation: BAA23389.1
AL009126 Genomic DNA Translation: CAB12627.1
PIRiB69807
RefSeqiNP_388679.1, NC_000964.3
WP_003244439.1, NZ_JNCM01000032.1

Genome annotation databases

EnsemblBacteriaiCAB12627; CAB12627; BSU07980
GeneIDi936136
KEGGibsu:BSU07980
PATRICifig|224308.179.peg.863

Entry informationi

Entry nameiPDAA_BACSU
AccessioniPrimary (citable) accession number: O34928
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 25, 2002
Last sequence update: January 1, 1998
Last modified: May 23, 2018
This is version 117 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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