Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

MetaCyc Enzyme: endo-1,4-β-xylanase XynZ

Gene: xynZ Accession Numbers: G-12722 (MetaCyc), Cthe_1963

Synonyms: 1,4-β-D-xylan xylanohydrolase Z, xylanase Z, Xyn10Z

Species: Ruminiclostridium thermocellum ATCC 27405

Component of:
fully loaded scaffoldin (cellobiose, high abundance catalytic units) (summary available)
cellulosome complex (or2p anchor, 18 most abundant catalytic units in cellobiose-grown cells) (extended summary available)

Summary:
The xynZ gene was first cloned in a study where ten distinct EcoRI fragments of Ruminiclostridium thermocellum, corresponding to seven different endoglucanases, were cloned in Escherichia coli and shown to express enzymatic activities related to cellulose degradation [Millet85]. Further analysis showed that the activity towards 4-methylumbelliferyl-β-D-cellobioside of some of the clones was due to xylanase rather than cellobiohydrolase activity [Grepinet88].

One of these clones, eventually named XynZ, confers on Escherichia coli the ability to hydrolyze xylan, 4-methylumbelliferyl-β-D-cellobioside, p-nitrophenyl-β-D-cellobioside, p-nitrophenyl-β-D-xylopyranoside, and p-nitrophenyl-β-D-xylobioside, but not carboxymethyl cellulose. The major end product of xylan hydrolysis was (1,4)-β-xylobiose.

The gene encoding the enzyme, xynZ, has been sequenced and analyzed [Grepinet88]. The cloned gene was expressed in Escherichia coli and purified. Using an antiserum raised against the purified enzyme an immunoreactive polypeptide of 90 kDa was detected in the Ruminiclostridium thermocellum cellulosome [Grepinet88a].

The gene contains a signal peptide, followed by several domains. Starting with the N terminus, XynZ has a feruloyl esterase domain, a proline-rich linker, a CBD6 carbohydrate-binding domain, a dockerin domain, and a glycosyl hydrolase family 10 (GH10) xylanase unit [Tokatlidis91, Grepinet88a, Blum00]. Feruloyl esterases are believed to aid in a release of lignin from hemicellulose. The crystal structure of the feruloyl esterase domain has been reported [Schubot01].

Recombinant versions of the protein with and without the dockerin domain were expressed in Escherichia coli. The truncated version expresses at a higher rate, up to 45% of total cell proteins. The specific activity of the enzyme without the non-catalytic domains was approximately 5-fold greater than that of the intact enzyme [Sajjad10].

Molecular Weight of Polypeptide: 92.263 kD (from nucleotide sequence), 90.0 kD (experimental) [Grepinet88a ]

Unification Links: Entrez-gene:4810746 , Protein Model Portal:P10478 , SMR:P10478 , String:203119.Cthe_1963 , UniProt:P10478

Relationship Links: CAZy:IN-FAMILY:CBM6 , CAZy:IN-FAMILY:GH10 , InterPro:IN-FAMILY:IPR000801 , InterPro:IN-FAMILY:IPR001000 , InterPro:IN-FAMILY:IPR002105 , InterPro:IN-FAMILY:IPR005084 , InterPro:IN-FAMILY:IPR006584 , InterPro:IN-FAMILY:IPR008979 , InterPro:IN-FAMILY:IPR013781 , InterPro:IN-FAMILY:IPR016134 , InterPro:IN-FAMILY:IPR017853 , InterPro:IN-FAMILY:IPR018242 , InterPro:IN-FAMILY:IPR018247 , PDB:Structure:1JJF , PDB:Structure:1JT2 , PDB:Structure:1XYZ , Pfam:IN-FAMILY:PF00331 , Pfam:IN-FAMILY:PF00404 , Pfam:IN-FAMILY:PF00756 , Pfam:IN-FAMILY:PF03422 , Prints:IN-FAMILY:PR00134 , Prosite:IN-FAMILY:PS00018 , Prosite:IN-FAMILY:PS00448 , Prosite:IN-FAMILY:PS00591 , Prosite:IN-FAMILY:PS51175 , Smart:IN-FAMILY:SM00606 , Smart:IN-FAMILY:SM00633

Gene-Reaction Schematic: ?

Credits:
Created 30-Mar-2011 by Caspi R , SRI International


Enzymatic reaction of: feruloyl esterase (endo-1,4-β-xylanase XynZ)

EC Number: 3.1.1.73

a feruloyl-polysaccharide + H2O <=> ferulate + a polysaccharide + 2 H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

In Pathways: cellulose and hemicellulose degradation (cellulolosome)

Summary:
Feruloyl esterases function in the cleavage of ferulic acid's bonds to arabinoxylan and pectin where the ferulic acid moieties cross-link the layers of polysaccharide chains within hemicellulose. Feruloyl esterases are believed to aid in a release of lignin from hemicellulose and may be involved in lignin solubilization. The presence of feruloyl esterase in the C. thermocellum cellulosome together with its other hydrolytic activities demonstrates a powerful enzymatic potential of this organelle in plant cell wall decomposition [Blum00].

The recombinant feruloyl esterase domain of XynZ alone can hydrolyze several feruloyl esters. Substrate that are similar but with a p-coumaroyl group instead of a feruloyl moiety was hydrolyzed at a rate 10 times slower. Treatment of Coastal Bermuda grass with the enzyme released mainly ferulic acid and a lower amount of p-coumaric acid [Blum00].

The crystal structure of the feruloyl esterase domain has been reported [Schubot01].

T(opt): 60 °C [Blum00]

pH(opt): 4-7 [Blum00]


Enzymatic reaction of: endo-1,4-β-xylanase

EC Number: 3.2.1.8

a (1→4)-β-D-xylan + n H2O <=> n a (1->4)-β-D-xylan oligosaccharide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for a (1→4)-β-D-xylan: 4-methylumbelliferyl-β-D-cellobioside [Grepinet88 ] , p-nitrophenyl-β-D-cellobioside [Grepinet88 ] , p-nitrophenyl-β-D-xylopyranoside [Grepinet88 ] , p-nitrophenyl-β-D-xylobioside [Grepinet88 ]

In Pathways: cellulose and hemicellulose degradation (cellulolosome)


Subunit of: fully loaded scaffoldin (cellobiose, high abundance catalytic units)

Species: Ruminiclostridium thermocellum ATCC 27405

Subunit composition of fully loaded scaffoldin (cellobiose, high abundance catalytic units) = [Cthe_0032][CelE][CelK][Cthe_0821][XghA][CelA][XynC][XynA][XynZ][CipA]
         glycosyl hydrolase family 26 domain protein = Cthe_0032 (summary available)
         cellulase E = CelE (extended summary available)
         cellulose 1,4-β-cellobiosidase (non-reducing end) = CelK (extended summary available)
         glycosyl hydrolase family 5 domain protein = Cthe_0821 (summary available)
         endo-β-1,4-glucanase XghA = XghA (extended summary available)
         cellulase A = CelA (extended summary available)
         endo-1,4-β-xylanase XynC = XynC (extended summary available)
         endo-1,4-β-xylanase XynA = XynA (extended summary available)
         endo-1,4-β-xylanase XynZ = XynZ (extended summary available)
         CipA scaffoldin = CipA (extended summary available)

Component of: cellulosome complex (or2p anchor, 18 most abundant catalytic units in cellobiose-grown cells) (extended summary available)

Summary:
This protein complex stands for a CipA scaffoldin protein loaded with the 9 most abundant catalytic cellulosomal proteins that are expressed in cells of Ruminiclostridium thermocellum grown on β-D-cellobiose (ratio of 14-5 mol catalytic unit per CipA molecule). The most abundant catalytic unit under these conditions is endo-1,4-β-xylanase XynZ, with a ratio of 14 XynZ/CipA [Gold07a].

Credits:
Created 04-Apr-2011 by Caspi R , SRI International


Subunit of: cellulosome complex (or2p anchor, 18 most abundant catalytic units in cellobiose-grown cells)

Species: Ruminiclostridium thermocellum ATCC 27405

Subunit composition of cellulosome complex (or2p anchor, 18 most abundant catalytic units in cellobiose-grown cells) = [Orf2p][(Cthe_0032)(CelE)(CelK)(Cthe_0821)(XghA)(CelA)(XynC)(XynA)(XynZ)(CipA)][(CipA)(CelB)(Cthe_2193)(XynD)(CelG)(CelR)(CelF)(CbhA)(Cthe_0405)(Cthe_1271)]
         anchoring scaffoldin Orf2p = Orf2p (extended summary available)
         fully loaded scaffoldin (cellobiose, high abundance catalytic units) = (Cthe_0032)(CelE)(CelK)(Cthe_0821)(XghA)(CelA)(XynC)(XynA)(XynZ)(CipA) (summary available)
                 glycosyl hydrolase family 26 domain protein = Cthe_0032 (summary available)
                 cellulase E = CelE (extended summary available)
                 cellulose 1,4-β-cellobiosidase (non-reducing end) = CelK (extended summary available)
                 glycosyl hydrolase family 5 domain protein = Cthe_0821 (summary available)
                 endo-β-1,4-glucanase XghA = XghA (extended summary available)
                 cellulase A = CelA (extended summary available)
                 endo-1,4-β-xylanase XynC = XynC (extended summary available)
                 endo-1,4-β-xylanase XynA = XynA (extended summary available)
                 endo-1,4-β-xylanase XynZ = XynZ (extended summary available)
                 CipA scaffoldin = CipA (extended summary available)
         fully loaded scaffoldin (cellobiose, medium abundance catalytic subunits) = (CipA)(CelB)(Cthe_2193)(XynD)(CelG)(CelR)(CelF)(CbhA)(Cthe_0405)(Cthe_1271) (summary available)
                 CipA scaffoldin = CipA (extended summary available)
                 cellulase B = CelB (extended summary available)
                 glycosyl hydrolase family 5 domain protein = Cthe_2193 (summary available)
                 endo-1,4-β-xylanase XynD = XynD (extended summary available)
                 cellulase G = CelG (extended summary available)
                 cellulase R = CelR (summary available)
                 cellulase F = CelF (extended summary available)
                 cellulose 1,4-β-cellobiosidase CbhA = CbhA (extended summary available)
                 glycosyl hydrolase family 5 domain protein = Cthe_0405 (summary available)
                 glycosyl hydrolase family 43 domain protein = Cthe_1271 (summary available)

Summary:
The strictly anerobic, thermophilic bacterium Ruminiclostridium thermocellum is the microorganism with the fastest growth rate on the recalcitrant substrate crystalline cellulose [Lynd02]. The higher efficiency of its extracellular hydrolytic machinery over that of other microorganisms is due to the formation of a huge enzyme complex, the cellulosome, which has a size of 18 nm diameter and a mass in excess of 2000 kDa [Shoham99].

The cellulosome is a modular complex. The center of the complex consists of a central non-catalytic protein known as the scaffoldin (CipA), which binds up to nine catalytic subunits [Wu88]. The attachment of each catalytic subunit is mediated by the interaction of its type I dockerin domain with one of the nine type I cohesin domains of CipA [Kruus95].

CipA is, in turn, bound to the cell surface by the interaction of its type II dockerin domain with the type II cohesin domain of one of three S-layer anchor proteins, SdbA, Orf2p, or OlpB [Bayer98]. Each of these anchor proteins contains a C-terminal S-layer homology module that mediates attachment to the bacterial cell surface, and a different number of type II cohesin modules capable of binding CipA molecules. Thus different anchoring scaffoldins form cellulosome complexes of differing sizes. The smallest one, anchoring scaffoldin SdbA, contains one cohesin domain, and thus binds one CipA molecule along with the nine catalytic units bound to it. The medium size anchoring scaffoldin Orf2p contains two cohesin domains and thus binds two CipA molecules and forms complexes with 18 catalytic units. The most abundant anchor protein is anchoring scaffoldin OlpB, which contains seven cohesin domains and forms complexes of up to 63 catalytic units.

In addition to nine type I cohesin domains and a type II dockerin domain, the CipA scaffoldin also contains a type III cellulose-binding module for attachment of the complex to cellulose [Gerngross93]. Many of the catalytic units also contain carbohydrate-binding domains with differing specificities.

The specific composition of the cellulosomes depends on growth rate and the nature of substrates available. In a 2007 experiment that identified cellulosome components under conditions of growth on either β-D-cellobiose or avicel [Gold07a], the following components were detected (in order of abundance):

Proteins detected in avicel-grown cells:

cellulose 1,4-β-cellobiosidase (non-reducing end), cellulose 1,4-β-cellobiosidase (reducing end), cellulase R, anchoring scaffoldin OlpB, Cthe_0821 glycosyl hydrolase family 5 domain protein, cellulase A, cellulase E, cellulase J, endo-1,4-β-xylanase XynC, endo-1,4-β-xylanase XynZ, cellulose 1,4-β-cellobiosidase CbhA, cellulase T, cellulase G, endo-1,4-β-xylanase XynA, endo-β-1,4-glucanase XghA, cellulase W, cellulase F, Cthe_0736 cellulosomal cohesin-domain protein, Cthe_2193 glycosyl hydrolase family 5 domain protein, licheninase LicB, mannanase A, cellulase Q, Cthe_0032 glycosyl hydrolase family 26 domain protein, cellulase B, anchoring scaffoldin Orf2p, cellulase P, Cthe_2761 glycosyl hydrolase family 9 domain protein, Cthe_0405 glycosyl hydrolase family 5 domain protein, cellulase N, cellulase D, glycoside hydrolase family 9 domain protein LecB, endochitinase ChiA, Cthe_1400 glycosyl hydrolase 53 domain protein, pectin lyase.

The following proteins were detected only in avicel-grown cells:

Cthe_0736 cellulosomal cohesin-domain protein, licheninase LicB, mannanase A, cellulase Q, cellulase P, cellulase N, and pectin lyase.

Proteins detected in cellobiose-grown cells:

endo-1,4-β-xylanase XynZ, CipA scaffoldin, endo-1,4-β-xylanase XynA, endo-1,4-β-xylanase XynC, cellulase A, endo-β-1,4-glucanase XghA, Cthe_0821 glycosyl hydrolase family 5 domain protein, cellulose 1,4-β-cellobiosidase (non-reducing end), cellulase E, Cthe_0032 glycosyl hydrolase family 26 domain protein, cellulase B, anchoring scaffoldin OlpB, Cthe_2193 glycosyl hydrolase family 5 domain protein, endo-1,4-β-xylanase XynD, cellulase G, cellulase R, cellulase F, cellulose 1,4-β-cellobiosidase CbhA, Cthe_0405 glycosyl hydrolase family 5 domain protein, Cthe_1271 glycosyl hydrolase family 43 domain protein, Cthe_2761 glycosyl hydrolase family 9 domain protein, cellulase T, cellulase W, cellulose 1,4-β-cellobiosidase (reducing end), endochitinase ChiA, cellulase J, Cthe_1400 glycosyl hydrolase 53 domain protein, glycoside hydrolase family 9 domain protein LecB, α-L-arabinofuranosidase B, anchoring scaffoldin Orf2p, cellulase D, anchoring scaffoldin SdbA, α-L-arabinofuranosidase B, endo-1,4-β-xylanase XynY.

The following proteins were detected only in β-D-cellobiose-grown cells:

endo-1,4-β-xylanase XynD, Cthe_1271 glycosyl hydrolase family 43 domain protein, α-L-arabinofuranosidase B, anchoring scaffoldin SdbA, α-L-arabinofuranosidase B and endo-1,4-β-xylanase XynY

Credits:
Created 04-Apr-2011 by Caspi R , SRI International


References

Bayer98: Bayer EA, Shimon LJ, Shoham Y, Lamed R (1998). "Cellulosomes-structure and ultrastructure." J Struct Biol 124(2-3);221-34. PMID: 10049808

Biely85: Biely P. (1985). "Microbial xylanolytic enzymes." Trends in Biotechnology.

Blum00: Blum DL, Kataeva IA, Li XL, Ljungdahl LG (2000). "Feruloyl esterase activity of the Clostridium thermocellum cellulosome can be attributed to previously unknown domains of XynY and XynZ." J Bacteriol 182(5);1346-51. PMID: 10671457

deVries01: de Vries RP, Visser J (2001). "Aspergillus enzymes involved in degradation of plant cell wall polysaccharides." Microbiol Mol Biol Rev 65(4);497-522, table of contents. PMID: 11729262

Gerngross93: Gerngross UT, Romaniec MP, Kobayashi T, Huskisson NS, Demain AL (1993). "Sequencing of a Clostridium thermocellum gene (cipA) encoding the cellulosomal SL-protein reveals an unusual degree of internal homology." Mol Microbiol 8(2);325-34. PMID: 8316083

Gold07a: Gold ND, Martin VJ (2007). "Global view of the Clostridium thermocellum cellulosome revealed by quantitative proteomic analysis." J Bacteriol 189(19);6787-95. PMID: 17644599

Gordillo06: Gordillo F, Caputo V, Peirano A, Chavez R, Van Beeumen J, Vandenberghe I, Claeyssens M, Bull P, Ravanal MC, Eyzaguirre J (2006). "Penicillium purpurogenum produces a family 1 acetyl xylan esterase containing a carbohydrate-binding module: characterization of the protein and its gene." Mycol Res 110(Pt 10);1129-39. PMID: 17008082

Grepinet88: Grepinet O, Chebrou MC, Beguin P (1988). "Nucleotide sequence and deletion analysis of the xylanase gene (xynZ) of Clostridium thermocellum." J Bacteriol 170(10);4582-8. PMID: 3139632

Grepinet88a: Grepinet O, Chebrou MC, Beguin P (1988). "Purification of Clostridium thermocellum xylanase Z expressed in Escherichia coli and identification of the corresponding product in the culture medium of C. thermocellum." J Bacteriol 170(10);4576-81. PMID: 3139631

Joseleau92: Joseleau J. P., Comptat J., Ruel K. (1992). "Chemical structure of xylans and their interaction in the plant cell wall." Progress in Biotechnology.

Kruus95: Kruus K, Lua AC, Demain AL, Wu JH (1995). "The anchorage function of CipA (CelL), a scaffolding protein of the Clostridium thermocellum cellulosome." Proc Natl Acad Sci U S A 92(20);9254-8. PMID: 7568112

Lynd02: Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002). "Microbial cellulose utilization: fundamentals and biotechnology." Microbiol Mol Biol Rev 66(3);506-77, table of contents. PMID: 12209002

Millet85: Millet, J., Petre, D., Beguin, P., Raynaud, O., Aubert, J. P. (1985). "Cloning of ten distinct DNA fragments of Clostridium thermocellum coding for cellulases (Endoglucanases, cellobiohydrolases, cellulolytic genes)." FEMS Microbiology Letters 29:145-149.

Sajjad10: Sajjad M, Khan MI, Akbar NS, Ahmad S, Ali I, Akhtar MW (2010). "Enhanced expression and activity yields of Clostridium thermocellum xylanases without non-catalytic domains." J Biotechnol 145(1);38-42. PMID: 19861138

Schadel10: Schadel C, Richter A, Blochl A, Hoch G (2010). "Hemicellulose concentration and composition in plant cell walls under extreme carbon source-sink imbalances." Physiol Plant 139(3);241-55. PMID: 20113432

Schubot01: Schubot FD, Kataeva IA, Blum DL, Shah AK, Ljungdahl LG, Rose JP, Wang BC (2001). "Structural basis for the substrate specificity of the feruloyl esterase domain of the cellulosomal xylanase Z from Clostridium thermocellum." Biochemistry 40(42);12524-32. PMID: 11601976

Shoham99: Shoham Y, Lamed R, Bayer EA (1999). "The cellulosome concept as an efficient microbial strategy for the degradation of insoluble polysaccharides." Trends Microbiol 7(7);275-81. PMID: 10390637

Tokatlidis91: Tokatlidis K, Salamitou S, Beguin P, Dhurjati P, Aubert JP (1991). "Interaction of the duplicated segment carried by Clostridium thermocellum cellulases with cellulosome components." FEBS Lett 291(2);185-8. PMID: 1936262

Wu88: Wu, J.H.D., Orme-Johnson, W.H., Demain, A.L. (1988). "Two components of an extracellular protein aggregate of Clostridium thermocellum together degrade crystalline cellulose." Biochemistry 27:1703-1709.


Report Errors or Provide Feedback
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 18.5 on Wed Nov 26, 2014, biocyc13.