cd10917

Catalytic NodB homology domain of rhizobial NodB-like proteins

CDD entry
Member databaseCDD
CDD typedomain
Short nameCE4_NodB_like_6s_7s
SetCE4_SF

Description

This family belongs to the large and functionally diverse carbohydrate esterase 4 (CE4) superfamily, whose members show strong sequence similarity with some variability due to their distinct carbohydrate substrates. It includes many rhizobial NodB chitooligosaccharide N-deacetylase (EC 3.5.1.-)-like proteins, mainly from bacteria and eukaryotes, such as chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan. All members of this family contain a catalytic NodB homology domain with the same overall topology and a deformed (beta/alpha)8 barrel fold with 6- or 7 strands. Their catalytic activity is dependent on the presence of a divalent cation, preferably cobalt or zinc, and they employ a conserved His-His-Asp zinc-binding triad closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. Several family members show diversity both in metal ion specificities and in the residues that coordinate the metal.
[25, 26, 9, 16, 10, 8, 24, 14, 23, 12, 17, 13, 15, 21, 20, 3, 11, 4, 6, 19, 1, 5, 18, 22, 2, 7]

References

1.Mode of action of chitin deacetylase from Mucor rouxii on N-acetylchitooligosaccharides. Tsigos I, Zydowicz N, Martinou A, Domard A, Bouriotis V. Eur J Biochem 261, 698-705, (1999). PMID: 10215886

2.Carbohydrate esterase family 4 enzymes: substrate specificity. Caufrier F, Martinou A, Dupont C, Bouriotis V. Carbohydr. Res. 338, 687-92, (2003). View articlePMID: 12644381

3.Recognition of chitooligosaccharides and their N-acetyl groups by putative subsites of chitin deacetylase from a deuteromycete, Colletotrichum lindemuthianum. Tokuyasu K, Mitsutomi M, Yamaguchi I, Hayashi K, Mori Y. Biochemistry 39, 8837-43, (2000). PMID: 10913295

4.The primary structure of a fungal chitin deacetylase reveals the function for two bacterial gene products. Kafetzopoulos D, Thireos G, Vournakis JN, Bouriotis V. Proc Natl Acad Sci U S A 90, 8005-8, (1993). PMID: 8367456

5.Structure and activity of two metal ion-dependent acetylxylan esterases involved in plant cell wall degradation reveals a close similarity to peptidoglycan deacetylases. Taylor EJ, Gloster TM, Turkenburg JP, Vincent F, Brzozowski AM, Dupont C, Shareck F, Centeno MS, Prates JA, Puchart V, Ferreira LM, Fontes CM, Biely P, Davies GJ. J. Biol. Chem. 281, 10968-75, (2006). View articlePMID: 16431911

6.Structure and mechanism of chitin deacetylase from the fungal pathogen Colletotrichum lindemuthianum. Blair DE, Hekmat O, Schuttelkopf AW, Shrestha B, Tokuyasu K, Withers SG, van Aalten DM. Biochemistry 45, 9416-26, (2006). View articlePMID: 16878976

7.Substrate specificity and mode of action of acetylxylan esterase from Streptomyces lividans. Biely P, Cote GL, Kremnicky L, Greene RV, Dupont C, Kluepfel D. FEBS Lett 396, 257-60, (1996). PMID: 8914998

8.Rhizobium-legume nodulation: life together in the underground. Long SR. Cell 56, 203-14, (1989). PMID: 2643474

9.The common nodABC genes of Rhizobium meliloti are host-range determinants. Roche P, Maillet F, Plazanet C, Debelle F, Ferro M, Truchet G, Prome JC, Denarie J. Proc Natl Acad Sci U S A 93, 15305-10, (1996). PMID: 8986807

10.Rhizobium NodB protein involved in nodulation signal synthesis is a chitooligosaccharide deacetylase. John M, Rohrig H, Schmidt J, Wieneke U, Schell J. Proc. Natl. Acad. Sci. U.S.A. 90, 625-9, (1993). View articlePMID: 8421697

11.Cloning and expression of two chitin deacetylase genes of Saccharomyces cerevisiae. Mishra C, Semino CE, McCreath KJ, de la Vega H, Jones BJ, Specht CA, Robbins PW. Yeast 13, 327-36, (1997). View articlePMID: 9133736

12.Cloning and characterization of the yjeA gene, encoding a novel deoxyribonuclease, from Bacillus subtilis. Ng KL, Lam CC, Fu Z, Han YF, Tsim KW, Wong WK. J Biochem 142, 647-54, (2007). PMID: 17878218

13.Structure and metal-dependent mechanism of peptidoglycan deacetylase, a streptococcal virulence factor. Blair DE, Schuttelkopf AW, MacRae JI, van Aalten DM. Proc. Natl. Acad. Sci. U.S.A. 102, 15429-34, (2005). View articlePMID: 16221761

14.Mode of action of acetylxylan esterase from Streptomyces lividans: a study with deoxy and deoxy-fluoro analogues of acetylated methyl beta-D-xylopyranoside. Biely P, Mastihubova M, Cote GL, Greene RV. Biochim Biophys Acta 1622, 82-8, (2003). PMID: 12880945

15.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 SJ, Sekiguchi J. J. Bacteriol. 184, 6007-15, (2002). View articlePMID: 12374835

16.Activity of Sinorhizobium meliloti NodAB and NodH enzymes on thiochitooligosaccharides. Southwick AM, Wang LX, Long SR, Lee YC. J Bacteriol 184, 4039-43, (2002). PMID: 12081977

17.The essential YycFG two-component system controls cell wall metabolism in Bacillus subtilis. Bisicchia P, Noone D, Lioliou E, Howell A, Quigley S, Jensen T, Jarmer H, Devine KM. Mol Microbiol 65, 180-200, (2007). PMID: 17581128

18.Identification of catalytically important amino acid residues of Streptomyces lividans acetylxylan esterase A from carbohydrate esterase family 4. Puchart V, Gariepy MC, Shareck F, Dupont C. Biochim Biophys Acta 1764, 263-74, (2006). PMID: 16434244

19.Bioconversion of chitin to chitosan: purification and characterization of chitin deacetylase from Mucor rouxii. Kafetzopoulos D, Martinou A, Bouriotis V. Proc Natl Acad Sci U S A 90, 2564-8, (1993). PMID: 8464862

20.Structure of a carbohydrate esterase from Bacillus anthracis. Oberbarnscheidt L, Taylor EJ, Davies GJ, Gloster TM. Proteins 66, 250-2, (2007). View articlePMID: 17063474

21.Structures of Bacillus subtilis PdaA, a family 4 carbohydrate esterase, and a complex with N-acetyl-glucosamine. Blair DE, van Aalten DM. FEBS Lett. 570, 13-9, (2004). View articlePMID: 15251431

22.The vicinal hydroxyl group is prerequisite for metal activation of Clostridium thermocellum acetylxylan esterase. Biely P, Mastihubova M, Puchart V. Biochim Biophys Acta 1770, 565-70, (2007). PMID: 17261352

23.The 172 kb prkA-addAB region from 83 degrees to 97 degrees of the Bacillus subtilis chromosome contains several dysfunctional genes, the glyB marker, many genes encoding transporter proteins, and the ubiquitous hit gene. Noback MA, Holsappel S, Kiewiet R, Terpstra P, Wambutt R, Wedler H, Venema G, Bron S. Microbiology (Reading) 144 ( Pt 4), 859-875, (1998). PMID: 9579061

24.Streptococcus mutans SMU.623c codes for a functional, metal-dependent polysaccharide deacetylase that modulates interactions with salivary agglutinin. Deng DM, Urch JE, ten Cate JM, Rao VA, van Aalten DM, Crielaard W. J. Bacteriol. 191, 394-402, (2009). View articlePMID: 18978064

25.Common nodABC genes in Nod locus 1 of Azorhizobium caulinodans: nucleotide sequence and plant-inducible expression. Goethals K, Gao M, Tomekpe K, Van Montagu M, Holsters M. Mol Gen Genet 219, 289-98, (1989). PMID: 2615763

26.Rhizobium meliloti nodA and nodB genes are involved in generating compounds that stimulate mitosis of plant cells. Schmidt J, Wingender R, John M, Wieneke U, Schell J. Proc Natl Acad Sci U S A 85, 8578-82, (1988). PMID: 16593994

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