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Escherichia coli K-12 substr. MG1655 Enzyme: poly-β-1,6-N-acetyl-D-glucosamine N-deacetylase



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

Synonyms: hmsF, ycdR

Regulation Summary Diagram: ?

Regulation summary diagram for pgaB

Summary:
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 [Wang04a, Itoh05, Itoh08].

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 [Wang04a, Itoh08].

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 [Wang05, 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 [Jones99].

Comment: [Kwan14]

Citations: [Agladze05]

Locations: outer membrane

Map Position: [1,087,062 <- 1,089,080] (23.43 centisomes, 84°)
Length: 2019 bp / 672 aa

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

Genetic Regulation Schematic: ?

Genetic regulation schematic for pgaB

GO Terms:

Biological Process: GO:0042710 - biofilm formation Inferred from experiment [Wang04a]
GO:0098732 - macromolecule deacylation Inferred from experiment [Itoh08, Little12]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Inferred from experiment Inferred by computational analysis [GOA01, Itoh08, Little12]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0009279 - cell outer membrane Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]
GO:0031246 - intrinsic component of periplasmic side of cell outer membrane Inferred by computational analysis [Itoh08, Wang04a]

MultiFun Terms: metabolism biosynthesis of macromolecules (cellular constituents)

Essentiality data for pgaB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Curated 31-Jul-2008 by Johnson A , JCVI
Last-Curated ? 18-Dec-2014 by Mackie A , Macquarie University


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.


Sequence Features

Protein sequence of poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase with features indicated

Feature Class Location Common Name Citations Comment
Signal-Sequence 1 -> 20 PgaB signal sequence
[Itoh08]
 
Chain 21 -> 672  
[UniProt09]
UniProt: Biofilm PGA synthesis lipoprotein pgaB;
Lipid-Binding-Site 21 PgaB palmitoylation site
[Itoh08]
 
Conserved-Region 107 -> 349  
[UniProt14]
UniProt: NodB homology.
Mutagenesis-Variant 115  
[Itoh08, UniProt11]
UniProt: High decrease in catalytic activity. Unable to support biofilm formation and PGA secretion.
Mutagenesis-Variant 184  
[Itoh08, UniProt11]
UniProt: Unable to support biofilm formation and PGA secretion.


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram

Notes:

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


References

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

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

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

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: 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

Itoh08: 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

Jones99: 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

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

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.

UniProt14: 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 manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

Wang04a: 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

Wang05: 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

Other References Related to Gene Regulation

Oropeza15: Oropeza R, Salgado-Bravo R, Calva E (2015). "Deletion analysis of RcsC reveals a novel signalling pathway controlling poly-N-acetylglucosamine synthesis and biofilm formation in Escherichia coli." Microbiology 161(Pt 4);903-13. PMID: 25667010


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Wed Jul 29, 2015, biocyc11.