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Protein

Peptidoglycan deacetylase

Gene

pgdA

Organism
Helicobacter pylori (strain G27)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the N-deacetylation of peptidoglycan (PG), an important mechanism that appears to confer lysozyme resistance and to mitigate host immune detection; this likely contributes to pathogen persistence in the host. The exact nature of the residue in PG that is deacetylated has not been determined. Is also able to catalyze the deacetylation of acetylated xylan, and, to a lesser extent, that of chitin and chitosan. Therefore, this enzyme might play a role during infection, considering that xylan-containing carbohydrate structures are among those commonly consumed by humans (By similarity). In vitro, does not show activity on N-acetylglucosamine (GlcNAc), chitotriose (GlcNAc3), some N-acetyl-dipeptides and allantoinase.By similarity1 Publication

Catalytic activityi

Deacetylation of xylans and xylo-oligosaccharides.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi14Zinc1 Publication1
Metal bindingi86Zinc; via tele nitrogen1 Publication1
Metal bindingi90Zinc; via tele nitrogen1 Publication1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Carbohydrate metabolism, Cell wall biogenesis/degradation, Polysaccharide degradation, Xylan degradation

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BRENDAi3.5.1.104. 2604.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptidoglycan deacetylase (EC:3.5.1.-)
Short name:
PG deacetylase
Alternative name(s):
Acetylxylan esterase (EC:3.1.1.72)
Gene namesi
Name:pgdA
Ordered Locus Names:HPG27_289
OrganismiHelicobacter pylori (strain G27)
Taxonomic identifieri563041 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
Proteomesi
  • UP000001735 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00004244392 – 293Peptidoglycan deacetylaseAdd BLAST292

Interactioni

Subunit structurei

Homotetramer.1 Publication

Structurei

Secondary structure

1293
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 12Combined sources9
Helixi15 – 21Combined sources7
Helixi29 – 40Combined sources12
Helixi42 – 52Combined sources11
Beta strandi58 – 61Combined sources4
Helixi63 – 68Combined sources6
Helixi70 – 78Combined sources9
Beta strandi82 – 85Combined sources4
Helixi93 – 95Combined sources3
Helixi98 – 116Combined sources19
Helixi126 – 128Combined sources3
Helixi133 – 139Combined sources7
Turni140 – 142Combined sources3
Beta strandi153 – 155Combined sources3
Beta strandi157 – 161Combined sources5
Helixi174 – 176Combined sources3
Beta strandi185 – 191Combined sources7
Helixi196 – 198Combined sources3
Helixi201 – 204Combined sources4
Helixi219 – 236Combined sources18
Beta strandi238 – 246Combined sources9
Helixi248 – 251Combined sources4
Helixi254 – 267Combined sources14
Beta strandi273 – 275Combined sources3
Helixi278 – 288Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3QBUX-ray2.57A/B/C/D1-293[»]
4LY4X-ray2.20A/B/C/D1-293[»]
ProteinModelPortaliB5ZA76.
SMRiB5ZA76.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini29 – 276NodB homologyPROSITE-ProRule annotationAdd BLAST248

Sequence similaritiesi

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

Phylogenomic databases

HOGENOMiHOG000251649.
OMAiAHGYSHE.
OrthoDBiPOG091H02A7.

Family and domain databases

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

Sequencei

Sequence statusi: Complete.

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

B5ZA76-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKEILVAYG VDIDAVAGWL GSYGGEDSPD DISRGLFAGE VGIPRLLKLF
60 70 80 90 100
KKYHLPATWF VPGHSIETFP EQMKMIVDAG HEVGAHGYSH ENPIAMSTKQ
110 120 130 140 150
EEDVLLKSVE LIKDLTGKAP TGYVAPWWEF SNITNELLLK HGFKYDHSLM
160 170 180 190 200
HNDFTPYYVR VGDSWSKIDY SLEAKDWMKP LIRGVETNLV EIPANWYLDD
210 220 230 240 250
LPPMMFIKKS PNSFGFVSPR DIGQMWIDQF DWVYREMDYA VFSMTIHPDV
260 270 280 290
SARPQVLLMH EKIIEHINKH EGVRWVTFNE IADDFLKRNP RKK
Length:293
Mass (Da):33,734
Last modified:November 25, 2008 - v1
Checksum:i6E0D479D83BB0498
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001173 Genomic DNA. Translation: ACI27056.1.
RefSeqiWP_001040423.1. NC_011333.1.

Genome annotation databases

EnsemblBacteriaiACI27056; ACI27056; HPG27_289.
KEGGihpg:HPG27_289.
PATRICi20598521. VBIHelPyl113476_0320.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001173 Genomic DNA. Translation: ACI27056.1.
RefSeqiWP_001040423.1. NC_011333.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3QBUX-ray2.57A/B/C/D1-293[»]
4LY4X-ray2.20A/B/C/D1-293[»]
ProteinModelPortaliB5ZA76.
SMRiB5ZA76.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACI27056; ACI27056; HPG27_289.
KEGGihpg:HPG27_289.
PATRICi20598521. VBIHelPyl113476_0320.

Phylogenomic databases

HOGENOMiHOG000251649.
OMAiAHGYSHE.
OrthoDBiPOG091H02A7.

Enzyme and pathway databases

BRENDAi3.5.1.104. 2604.

Family and domain databases

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

Entry informationi

Entry nameiPGDAE_HELPG
AccessioniPrimary (citable) accession number: B5ZA76
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2013
Last sequence update: November 25, 2008
Last modified: November 2, 2016
This is version 52 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

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.