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Escherichia coli K-12 substr. MG1655 Polypeptide: poly-β-1,6-N-acetyl-D-glucosamine synthase - PgaD subunit



Gene: pgaD Accession Numbers: G6528 (EcoCyc), b1021, ECK1011

Synonyms: hmsS, ycdP

Regulation Summary Diagram: ?

Component of: poly-β-1,6-N-acetyl-D-glucosamine synthase (extended summary available)

Locations: inner membrane

Map Position: [1,085,329 <- 1,085,742] (23.39 centisomes)
Length: 414 bp / 137 aa

Molecular Weight of Polypeptide: 16.082 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003460 , DIP:DIP-48114N , EchoBASE:EB3622 , EcoGene:EG13862 , EcoliWiki:b1021 , OU-Microarray:b1021 , PortEco:pgaD , PR:PRO_000023522 , Protein Model Portal:P69432 , RefSeq:NP_415540 , RegulonDB:G6528 , String:511145.b1021 , UniProt:P69432

Relationship Links: InterPro:IN-FAMILY:IPR023829 , Pfam:IN-FAMILY:PF13994

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0043708 - cell adhesion involved in biofilm formation Inferred from experiment [Itoh08, Wang04]
GO:0042710 - biofilm formation Inferred by computational analysis [GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Steiner13, Butland05]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
GO:0005887 - integral component of plasma membrane Inferred by computational analysis [Wang04, Steiner13]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: metabolism biosynthesis of macromolecules (cellular constituents)

Essentiality data for pgaD 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:
Last-Curated ? 31-Jul-2008 by Johnson A , JCVI


Subunit of: poly-β-1,6-N-acetyl-D-glucosamine synthase

Synonyms: UDP-N-acetyl-D-glucosamine β-1,6-N-acetyl-D-glucosaminyl transferase, PgaCD

Subunit composition of poly-β-1,6-N-acetyl-D-glucosamine synthase = [PgaD][PgaC]
         poly-β-1,6-N-acetyl-D-glucosamine synthase - PgaD subunit = PgaD
         poly-β-1,6-N-acetyl-D-glucosamine synthase - PgaC subunit = PgaC

Summary:
PgaCD is a β-glycosyltransferase which polymerises poly-N-acetyl glucosamine (PGA), an adhesin essential in biofilm formation, from an activated UDP-N-acetyl-D-glucosamine (UDP-GlcNAc) precursor [Wang04] and transports it across the inner membrane for deacetylation and export by the OM proteins PgaB and PgaA.

PgaC and PgaD form a stable complex [Steiner13]. The second messenger cyclic di-3',5'-guanylate (c-di-GMP) stimulates PgaC-PgaD interaction and complex stability. c-di-GMP binds concurrently to PgaC-PgaD in vitro and no specific binding is observed in membranes containing only PgaC or PgaD. The binding of c-di-GMP to PgaCD increases in the presence of UDP-GlcNAc [Steiner13]. PgaD levels decrease in a strain lacking PgaC but are restored in a c-di-GMP manner when pgaC is expressed from a plasmid. PgaD levels decrease in a strain lacking diguanylate cyclase. c-di-GMP binds to PgaCD with high affinity, increasing the enzyme's velocity but not its affinity for substrate. c-di-GMP is an allosteric activator and stimulates the glycosyltransferase activity of PgaCD approximately 20-fold in vitro [Steiner13].

pgaC and pgaD mutants show reduced biofilm formation and do not accumulate PGA in a crsA background compared to wild-type [Wang04, Itoh08]. PgaC contains 4 predicted trans-membrane domains plus 2 membrane-associated domains; PgaD contains 2 predicted trans-membrane domains. PgaC also contains 2 catalytic domains predicted to be in the cytoplasm. The N and C-termini of both proteins are predicted to be in the cytoplasm [Wang04, Steiner13].

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]. Expression of pgaC increased in response to luxS deletion at OD 2.4 in LB [Wang05a].

PgaC has similarity to the HmsR protein encoded by the Yersinia pestis hmsHFRST gene cluster, which is involved in plague transmission [Jones99]. E. coli PgaC functionally complements the hemin storage (Hms) phenotype of a Yersinia pestis hmsR mutant [Jones99].

Review: [Hengge13]

Citations: [Itoh05]

Locations: inner membrane

GO Terms:

Biological Process: GO:0015774 - polysaccharide transport Inferred from experiment [Steiner13]
GO:0043708 - cell adhesion involved in biofilm formation Inferred from experiment [Wang04]
Molecular Function: GO:0015159 - polysaccharide transmembrane transporter activity Inferred from experiment [Steiner13]
GO:0008375 - acetylglucosaminyltransferase activity Inferred by computational analysis [Wang04]
Cellular Component: GO:0005887 - integral component of plasma membrane Inferred by computational analysis [Wang04, Steiner13]

Credits:
Created 09-Jan-2013 by Mackie A , Macquarie University
Last-Curated ? 09-Jan-2013 by Mackie A , Macquarie University


Enzymatic reaction of: transport of poly-β-1,6-N-acetyl-D-glucosamine (poly-β-1,6-N-acetyl-D-glucosamine synthase)


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

UDP-N-acetyl-α-D-glucosamine <=> poly-β-1,6-N-acetyl-D-glucosamine + UDP

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.

Activators (Allosteric): cyclic di-3',5'-guanylate [Steiner13]

Primary Physiological Regulators of Enzyme Activity: cyclic di-3',5'-guanylate

Kinetic Parameters:

Substrate
Km (μM)
Citations
UDP-N-acetyl-α-D-glucosamine
270.0
[Steiner13]


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 24 -> 44
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 54 -> 74
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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


References

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

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

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

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

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

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

Hengge13: Hengge R (2013). "Novel tricks played by the second messenger c-di-GMP in bacterial biofilm formation." EMBO J 32(3);322-3. PMID: 23299943

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

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

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Steiner13: Steiner S, Lori C, Boehm A, Jenal U (2013). "Allosteric activation of exopolysaccharide synthesis through cyclic di-GMP-stimulated protein-protein interaction." EMBO J 32(3);354-68. PMID: 23202856

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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

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

Wang05a: Wang L, Li J, March JC, Valdes JJ, Bentley WE (2005). "luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling." J Bacteriol 187(24);8350-60. PMID: 16321939


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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 18.5 on Sat Dec 20, 2014, biocyc13.