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Protein

Peptidoglycan-N-acetylmuramic acid deacetylase PdaA

Gene

pdaA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-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

pH dependencei

Optimum pH is 7.0.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei73 – 731Proton acceptorBy similarity
Metal bindingi124 – 1241Divalent metal cation; via tele nitrogen
Metal bindingi128 – 1281Divalent metal cation; via tele nitrogen
Sitei193 – 1931Raises pKa of active site HisBy similarity
Active sitei222 – 2221Proton donorBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Cell wall biogenesis/degradation, Sporulation

Keywords - Ligandi

Metal-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

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2323Sequence analysisAdd
BLAST
Chaini24 – 263240Peptidoglycan-N-acetylmuramic acid deacetylase PdaAPRO_0000024842Add
BLAST

Proteomic databases

PaxDbiO34928.

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

1
263
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi46 – 549Combined sources
Beta strandi58 – 603Combined sources
Beta strandi65 – 7612Combined sources
Helixi81 – 9010Combined sources
Beta strandi96 – 994Combined sources
Helixi101 – 1066Combined sources
Helixi108 – 1169Combined sources
Beta strandi120 – 1234Combined sources
Helixi131 – 1333Combined sources
Helixi136 – 15419Combined sources
Helixi165 – 1673Combined sources
Helixi171 – 1799Combined sources
Beta strandi183 – 1853Combined sources
Helixi196 – 1983Combined sources
Helixi202 – 21110Combined sources
Beta strandi217 – 2215Combined sources
Helixi228 – 24215Combined sources
Beta strandi245 – 2473Combined sources
Helixi249 – 2579Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 24-258.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO34928.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini66 – 247182NodB homologyPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the polysaccharide deacetylase family.Curated
Contains 1 NodB homology domain.PROSITE-ProRule annotation

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiCOG0726. LUCA.
HOGENOMiHOG000260720.
InParanoidiO34928.
KOiK01567.
OMAiYTNVFWS.
OrthoDBiEOG6V1M8Q.
PhylomeDBiO34928.

Family and domain databases

Gene3Di3.20.20.370. 1 hit.
InterProiIPR011330. Glyco_hydro/deAcase_b/a-brl.
IPR002509. NODB_dom.
IPR014235. Spore_PdaA.
[Graphical view]
PfamiPF01522. Polysacc_deac_1. 1 hit.
[Graphical view]
SUPFAMiSSF88713. SSF88713. 1 hit.
TIGRFAMsiTIGR02884. spore_pdaA. 1 hit.
PROSITEiPS51677. NODB. 1 hit.
[Graphical view]

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.
PATRICi18973246. VBIBacSub10457_0837.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 24-258.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100004443.

Proteomic databases

PaxDbiO34928.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12627; CAB12627; BSU07980.
GeneIDi936136.
KEGGibsu:BSU07980.
PATRICi18973246. VBIBacSub10457_0837.

Phylogenomic databases

eggNOGiCOG0726. LUCA.
HOGENOMiHOG000260720.
InParanoidiO34928.
KOiK01567.
OMAiYTNVFWS.
OrthoDBiEOG6V1M8Q.
PhylomeDBiO34928.

Enzyme and pathway databases

BioCyciBSUB:BSU07980-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO34928.

Family and domain databases

Gene3Di3.20.20.370. 1 hit.
InterProiIPR011330. Glyco_hydro/deAcase_b/a-brl.
IPR002509. NODB_dom.
IPR014235. Spore_PdaA.
[Graphical view]
PfamiPF01522. Polysacc_deac_1. 1 hit.
[Graphical view]
SUPFAMiSSF88713. SSF88713. 1 hit.
TIGRFAMsiTIGR02884. spore_pdaA. 1 hit.
PROSITEiPS51677. NODB. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and sequencing of a 40.6 kb segment in the 73 degrees-76 degrees region of the Bacillus subtilis chromosome containing genes for trehalose metabolism and acetoin utilization."
    Yamamoto H., Uchiyama S., Sekiguchi J.
    Microbiology 142:3057-3065(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / AC327.
  2. "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.
  3. "A polysaccharide deacetylase gene (pdaA) is required for germination and for production of muramic delta-lactam residues in the spore cortex of Bacillus subtilis."
    Fukushima T., Yamamoto H., Atrih A., Foster S.J., Sekiguchi J.
    J. Bacteriol. 184:6007-6015(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE.
    Strain: 168.
  4. "Production of muramic delta-lactam in Bacillus subtilis spore peptidoglycan."
    Gilmore M.E., Bandyopadhyay D., Dean A.M., Linnstaedt S.D., Popham D.L.
    J. Bacteriol. 186:80-89(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
  5. "A polysaccharide deacetylase homologue, PdaA, in Bacillus subtilis acts as an N-acetylmuramic acid deacetylase in vitro."
    Fukushima T., Kitajima T., Sekiguchi J.
    J. Bacteriol. 187:1287-1292(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, PH DEPENDENCE.
    Strain: 168 and ATCC 6633 / PCI 219 / NRS 231.
  6. "Structures of Bacillus subtilis PdaA, a family 4 carbohydrate esterase, and a complex with N-acetyl-glucosamine."
    Blair D.E., van Aalten D.M.
    FEBS Lett. 570:13-19(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH N-ACETYLGLUCOSAMINE AND CADMIUM.
  7. "Crystal structure of polysaccharide deacetylase (pdaa_bacsu) from B. subtilis (pdaa_bacsu) Northeast structural genomics research consortium (NESG) target sr127."
    Northeast structural genomics consortium (NESG)
    Submitted (FEB-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 24-263.

Entry informationi

Entry nameiPDAA_BACSU
AccessioniPrimary (citable) accession number: O34928
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 25, 2002
Last sequence update: January 1, 1998
Last modified: February 17, 2016
This is version 108 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

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

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

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.