MetaCyc Enzyme: poly-β-1,6-N-acetyl-D-glucosamine N-deacetylase

Gene: pgaB Accession Numbers: G6530 (MetaCyc), b1023, ECK1013

Synonyms: hmsF, ycdR

Species: Escherichia coli K-12 substr. MG1655

PgaB is an outer membrane lipoprotein that is required for the partial de-N-acetylation and transport of poly-β-1,6-N-acetyl-D-glucosamine (known as PGA or PNAG) - an exopolysaccharide that is a key component of the biofilm matrix of several medically important bacteria [Wang04, Itoh05, Itoh08a].

PgaB consists of an N-terminal domain that forms a (β/α)7 barrel structure and belongs to the class 4 carbohydrate esterases and a C-terminal domain that forms a (β/α)8 barrel and contains a flexible β hairpin loop [Little12]. Both domains are necessary for de-N-acetylation of PNAG; PNAG binds to a cleft formed between the N and C-terminal domains in an extended conformation [Little14].

PgaB is a metal dependent de-N-acetylase with a preference for Co2+, Ni2+ and Fe2+; PgaB binds two metal ions per molecule; PgaB has specificity for PNAG oligomers [Little12]

Deletion of pgaB results in reduced biofilm formation and retention of acetylated polymer in the periplasm; deacetylation of PNAG by PgaB promotes its export [Wang04, Itoh08a].

pgaB is part of a 4 gene locus (pgaABCD) whose gene products are involved in the synthesis, modification and export of PNAG. Expression of pgaABCD is higher at 37°C than at 21°C and is highest during stationary phase [Cerca08]. Expression also increased in response to one-percent NaCl or ethanol [Cerca08]. Expression increased in response to glucose, ethanol, NaCl, and MnCl2 in a clinical isolate, and dramatically increased upon deletion or mutation of csrA in this strain [Cerca08, Mercante06]. CsrA inhibits translation of pgaABCD mRNA by binding to six sites within the pgaABCD leader [Wang05d, Mercante06]. NaCl and alkaline pH induction are dependent upon nhaR as deletion of this gene prevented induction [Goller06, Cerca08].

PgaB has similarity to the HmsF protein encoded by the Yersinia pestis hmsHFRST gene cluster, which is involved in plague transmission [Jones99a].

Comment: [Kwan14]

Citations: [Agladze05]

Locations: outer membrane

Map Position: [1,087,062 <- 1,089,080]

Molecular Weight of Polypeptide: 77.413 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003467 , DIP:DIP-11513N , EchoBASE:EB3624 , EcoGene:EG13864 , EcoliWiki:b1023 , ModBase:P75906 , OU-Microarray:b1023 , PortEco:pgaB , Protein Model Portal:P75906 , RefSeq:NP_415542 , RegulonDB:G6530 , SMR:P75906 , String:511145.b1023 , UniProt:P75906

Relationship Links: InterPro:IN-FAMILY:IPR002509 , InterPro:IN-FAMILY:IPR011330 , InterPro:IN-FAMILY:IPR023854 , PDB:Structure:3VUS , PDB:Structure:4F9D , PDB:Structure:4F9J , PDB:Structure:4P7L , PDB:Structure:4P7N , PDB:Structure:4P7O , PDB:Structure:4P7Q , PDB:Structure:4P7R , Pfam:IN-FAMILY:PF01522 , Prosite:IN-FAMILY:PS51257 , Prosite:IN-FAMILY:PS51677

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0042710 - biofilm formation Inferred from experiment [Wang04]
GO:0098732 - macromolecule deacylation Inferred from experiment [Itoh08a, Little12]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Inferred from experiment Inferred by computational analysis [GOA01a, Itoh08a, Little12]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0009279 - cell outer membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0031246 - intrinsic component of periplasmic side of cell outer membrane Inferred by computational analysis [Itoh08a, Wang04]

MultiFun Terms: metabolism biosynthesis of macromolecules (cellular constituents)

Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

Enzymatic reaction of: poly-β-1,6-N-acetyl-D-glucosamine N-deacetylase

poly-β-1,6-N-acetyl-D-glucosamine + H2O <=> partially N-deacetylated poly-β-1,6-N-acetyl-D-glucosamine + acetate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

Reversibility of this reaction is unspecified.

Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

Sequence Features

Feature Class Location Common Name Citations Comment
Signal-Sequence 1 -> 20 PgaB signal sequence
Chain 21 -> 672  
UniProt: Biofilm PGA synthesis lipoprotein pgaB;
Lipid-Binding-Site 21 PgaB palmitoylation site
Conserved-Region 107 -> 349  
UniProt: NodB homology.
Mutagenesis-Variant 115  
[Itoh08a, UniProt11]
UniProt: High decrease in catalytic activity. Unable to support biofilm formation and PGA secretion.
Mutagenesis-Variant 184  
[Itoh08a, UniProt11]
UniProt: Unable to support biofilm formation and PGA secretion.

Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Agladze05: Agladze K, Wang X, Romeo T (2005). "Spatial periodicity of Escherichia coli K-12 biofilm microstructure initiates during a reversible, polar attachment phase of development and requires the polysaccharide adhesin PGA." J Bacteriol 187(24);8237-46. PMID: 16321928

Cerca08: Cerca N, Jefferson KK (2008). "Effect of growth conditions on poly-N-acetylglucosamine expression and biofilm formation in Escherichia coli." FEMS Microbiol Lett 283(1);36-41. PMID: 18445167

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Goller06: Goller C, Wang X, Itoh Y, Romeo T (2006). "The cation-responsive protein NhaR of Escherichia coli activates pgaABCD transcription, required for production of the biofilm adhesin poly-beta-1,6-N-acetyl-D-glucosamine." J Bacteriol 188(23);8022-32. PMID: 16997959

Itoh05: Itoh Y, Wang X, Hinnebusch BJ, Preston JF, Romeo T (2005). "Depolymerization of beta-1,6-N-acetyl-D-glucosamine disrupts the integrity of diverse bacterial biofilms." J Bacteriol 187(1);382-7. PMID: 15601723

Itoh08a: Itoh Y, Rice JD, Goller C, Pannuri A, Taylor J, Meisner J, Beveridge TJ, Preston JF, Romeo T (2008). "Roles of pgaABCD genes in synthesis, modification, and export of the Escherichia coli biofilm adhesin poly-beta-1,6-N-acetyl-D-glucosamine." J Bacteriol 190(10);3670-80. PMID: 18359807

Jones99a: Jones HA, Lillard JW, Perry RD (1999). "HmsT, a protein essential for expression of the haemin storage (Hms+) phenotype of Yersinia pestis." Microbiology 145 ( Pt 8);2117-28. PMID: 10463178

Kwan14: Kwan DH, Withers SG (2014). "Periplasmic de-acylase helps bacteria don their biofilm coat." Proc Natl Acad Sci U S A 111(30);10904-5. PMID: 25006258

Little12: Little DJ, Poloczek J, Whitney JC, Robinson H, Nitz M, Howell PL (2012). "The structure- and metal-dependent activity of Escherichia coli PgaB provides insight into the partial de-N-acetylation of poly-β-1,6-N-acetyl-D-glucosamine." J Biol Chem 287(37);31126-37. PMID: 22810235

Little14: Little DJ, Li G, Ing C, DiFrancesco BR, Bamford NC, Robinson H, Nitz M, Pomes R, Howell PL (2014). "Modification and periplasmic translocation of the biofilm exopolysaccharide poly-β-1,6-N-acetyl-D-glucosamine." Proc Natl Acad Sci U S A 111(30);11013-8. PMID: 24994902

Mercante06: Mercante J, Suzuki K, Cheng X, Babitzke P, Romeo T (2006). "Comprehensive alanine-scanning mutagenesis of Escherichia coli CsrA defines two subdomains of critical functional importance." J Biol Chem 281(42);31832-42. PMID: 16923806

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt14a: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wang04: Wang X, Preston JF, Romeo T (2004). "The pgaABCD locus of Escherichia coli promotes the synthesis of a polysaccharide adhesin required for biofilm formation." J Bacteriol 186(9);2724-34. PMID: 15090514

Wang05d: Wang X, Dubey AK, Suzuki K, Baker CS, Babitzke P, Romeo T (2005). "CsrA post-transcriptionally represses pgaABCD, responsible for synthesis of a biofilm polysaccharide adhesin of Escherichia coli." Mol Microbiol 56(6);1648-63. PMID: 15916613

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 19.0 on Wed Oct 7, 2015, biocyc12.