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PDBsum entry 1xyn

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protein metals links
Hydrolase PDB id
1xyn
Jmol
Contents
Protein chain
178 a.a. *
Metals
_CA
Waters ×80
* Residue conservation analysis
PDB id:
1xyn
Name: Hydrolase
Title: Structural comparison of two major endo-1,4-beta-xylanases from trichodrema reesei
Structure: Endo-1,4-beta-xylanase i. Chain: a. Synonym: xyni. Ec: 3.2.1.8
Source: Hypocrea jecorina. Organism_taxid: 51453. Strain: rut-c30
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.185    
Authors: J.Rouvinen,A.Torronen
Key ref:
A.Törrönen and J.Rouvinen (1995). Structural comparison of two major endo-1,4-xylanases from Trichoderma reesei. Biochemistry, 34, 847-856. PubMed id: 7827044 DOI: 10.1021/bi00003a019
Date:
09-Aug-94     Release date:   08-Aug-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P36218  (XYN1_HYPJE) -  Endo-1,4-beta-xylanase 1
Seq:
Struc:
229 a.a.
178 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.8  - Endo-1,4-beta-xylanase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1021/bi00003a019 Biochemistry 34:847-856 (1995)
PubMed id: 7827044  
 
 
Structural comparison of two major endo-1,4-xylanases from Trichoderma reesei.
A.Törrönen, J.Rouvinen.
 
  ABSTRACT  
 
Three-dimensional structures of two major endo-1,4-xylanases, XYNI and XYNII from Trichoderma reesei, have been determined by X-ray crystallography. The amino acid sequences of both enzymes are highly homologous (identity approximately 50%), and both XYNI and XYNII exist as a single domain that contains two mostly antiparallel beta-sheets which are packed against each other. The beta-sheet structure is twisted, forming a cleft where the active site is situated. Two glutamic acids in the cleft, Glu75 and Glu164 in XYNI as well as Glu86 and Glu177 in XYNII, are most likely involved in catalysis. Inspection of the structures reveals that the width of the active site cleft and the number of subsites are different in XYNI and XYNII. The active site is narrower in XYNI and probably contains only three subsites, whereas the number of subsites in XYNII is most likely five. Variations in the surroundings of catalytic residue Glu164XYNI/Glu177XYNII are thought to explain the pH optimum differences observed in XYNI and XYNII.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21269479 M.Rostkowski, M.H.Olsson, C.R.Søndergaard, and J.H.Jensen (2011).
Graphical analysis of pH-dependent properties of proteins predicted using PROPKA.
  BMC Struct Biol, 11, 6.  
20225927 A.Pollet, J.A.Delcour, and C.M.Courtin (2010).
Structural determinants of the substrate specificities of xylanases from different glycoside hydrolase families.
  Crit Rev Biotechnol, 30, 176-191.  
20122183 S.Mitra, M.Schubach, and D.H.Huson (2010).
Short clones or long clones? A simulation study on the use of paired reads in metagenomics.
  BMC Bioinformatics, 11, S12.  
19422059 A.Pollet, E.Vandermarliere, J.Lammertyn, S.V.Strelkov, J.A.Delcour, and C.M.Courtin (2009).
Crystallographic and activity-based evidence for thumb flexibility and its relevance in glycoside hydrolase family 11 xylanases.
  Proteins, 77, 395-403.
PDB code: 3exu
19769747 A.Pollet, S.Sansen, G.Raedschelders, K.Gebruers, A.Rabijns, J.A.Delcour, and C.M.Courtin (2009).
Identification of structural determinants for inhibition strength and specificity of wheat xylanase inhibitors TAXI-IA and TAXI-IIA.
  FEBS J, 276, 3916-3927.
PDB codes: 2b42 3hd8
19156310 M.E.Soliman, G.D.Ruggiero, J.J.Pernía, I.R.Greig, and I.H.Williams (2009).
Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformation for the substrate: QM/MM molecular dynamics studies of wild-type and mutant xylanases.
  Org Biomol Chem, 7, 460-468.  
19352037 P.Jommuengbout, S.Pinitglang, K.L.Kyu, and K.Ratanakhanokchai (2009).
Substrate-binding site of family 11 xylanase from Bacillus firmus K-1 by molecular docking.
  Biosci Biotechnol Biochem, 73, 833-839.  
19805272 S.Le Crom, W.Schackwitz, L.Pennacchio, J.K.Magnuson, D.E.Culley, J.R.Collett, J.Martin, I.S.Druzhinina, H.Mathis, F.Monot, B.Seiboth, B.Cherry, M.Rey, R.Berka, C.P.Kubicek, S.E.Baker, and A.Margeot (2009).
Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing.
  Proc Natl Acad Sci U S A, 106, 16151-16156.  
18384043 G.André-Leroux, J.G.Berrin, J.Georis, F.Arnaut, and N.Juge (2008).
Structure-based mutagenesis of Penicillium griseofulvum xylanase using computational design.
  Proteins, 72, 1298-1307.  
18292971 Q.Wang, and T.Xia (2008).
Enhancement of the activity and alkaline pH stability of Thermobifida fusca xylanase A by directed evolution.
  Biotechnol Lett, 30, 937-944.  
18025557 A.J.Afzal, S.A.Bokhari, and K.S.Siddiqui (2007).
Kinetic and thermodynamic study of a chemically modified highly active xylanase from Scopulariopsis sp: existence of an essential amino group.
  Appl Biochem Biotechnol, 141, 273-297.  
17216454 J.G.Berrin, e.l. .H.Ajandouz, J.Georis, F.Arnaut, and N.Juge (2007).
Substrate and product hydrolysis specificity in family 11 glycoside hydrolases: an analysis of Penicillium funiculosum and Penicillium griseofulvum xylanases.
  Appl Microbiol Biotechnol, 74, 1001-1010.  
17704573 N.Moiseeva, and M.Allaire (2007).
Using barium ions for heavy-atom derivatization and phasing of xylanase II from Trichoderma longibrachiatum.
  Acta Crystallogr D Biol Crystallogr, 63, 1025-1028.  
16906388 A.Cano, E.A.Moschou, S.Daunert, J.Coello, and C.Palet (2006).
Optimization of the xylan degradation activity of monolithic enzymatic membranes as a function of their composition using design of experiments.
  Bioprocess Biosyst Eng, 29, 261-268.  
16652352 M.Kozak (2006).
Solution scattering studies of conformation stability of xylanase XYNII from Trichoderma longibrachiatum.
  Biopolymers, 83, 95.  
16983650 M.Kozak (2006).
Synchrotron radiation small angle scattering studies of thermal stability of xylanase XYNII from Trichoderma longibrachiatum.
  Biopolymers, 83, 668-674.  
16790934 N.Watanabe, T.Akiba, R.Kanai, and K.Harata (2006).
Structure of an orthorhombic form of xylanase II from Trichoderma reesei and analysis of thermal displacement.
  Acta Crystallogr D Biol Crystallogr, 62, 784-792.
PDB codes: 2dfb 2dfc
16520923 W.Ogasawara, Y.Shida, T.Furukawa, R.Shimada, S.Nakagawa, M.Kawamura, T.Yagyu, A.Kosuge, J.Xu, M.Nogawa, H.Okada, and Y.Morikawa (2006).
Cloning, functional expression and promoter analysis of xylanase III gene from Trichoderma reesei.
  Appl Microbiol Biotechnol, 72, 995.  
15933005 C.Gauthier, H.Li, and R.Morosoli (2005).
Increase in xylanase production by Streptomyces lividans through simultaneous use of the Sec- and Tat-dependent protein export systems.
  Appl Environ Microbiol, 71, 3085-3092.  
16116276 H.Shibuya, S.Kaneko, and K.Hayashi (2005).
A single amino acid substitution enhances the catalytic activity of family 11 xylanase at alkaline pH.
  Biosci Biotechnol Biochem, 69, 1492-1497.  
16473771 H.Tanaka, T.Nakamura, S.Hayashi, and K.Ohta (2005).
Purification and properties of an extracellular endo-1,4-beta-xylanase from Penicillium citrinum and characterization of the encoding gene.
  J Biosci Bioeng, 100, 623-630.  
15853815 J.Jänis, J.Hakanpää, N.Hakulinen, F.M.Ibatullin, A.Hoxha, P.J.Derrick, J.Rouvinen, and P.Vainiotalo (2005).
Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography.
  FEBS J, 272, 2317-2333.
PDB code: 1xnk
15981262 M.D.Daily, D.Masica, A.Sivasubramanian, S.Somarouthu, and J.J.Gray (2005).
CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock.
  Proteins, 60, 181-186.  
  16510999 M.T.Murakami, R.Ruller, R.J.Ward, and R.K.Arni (2005).
Crystallization and preliminary X-ray crystallographic studies of the mesophilic xylanase A from Bacillus subtilis 1A1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 219-220.  
15652973 T.Collins, C.Gerday, and G.Feller (2005).
Xylanases, xylanase families and extremophilic xylanases.
  FEMS Microbiol Rev, 29, 3.  
15452343 C.L.Hansen, M.O.Sommer, and S.R.Quake (2004).
Systematic investigation of protein phase behavior with a microfluidic formulator.
  Proc Natl Acad Sci U S A, 101, 14431-14436.  
15213390 N.Moiseeva, and M.Allaire (2004).
Crystals of family 11 xylanase II from Trichoderma longibrachiatum that diffract to atomic resolution.
  Acta Crystallogr D Biol Crystallogr, 60, 1275-1277.  
15451095 T.A.Tahir, A.Durand, K.Gebruers, A.Roussel, G.Williamson, and N.Juge (2004).
Functional importance of Asp37 from a family 11 xylanase in the binding to two proteinaceous xylanase inhibitors from wheat.
  FEMS Microbiol Lett, 239, 9.  
14993687 T.Parkkinen, N.Hakulinen, M.Tenkanen, M.Siika-aho, and J.Rouvinen (2004).
Crystallization and preliminary X-ray analysis of a novel Trichoderma reesei xylanase IV belonging to glycoside hydrolase family 5.
  Acta Crystallogr D Biol Crystallogr, 60, 542-544.  
12657781 A.J.Oakley, T.Heinrich, C.A.Thompson, and M.C.Wilce (2003).
Characterization of a family 11 xylanase from Bacillus subtillis B230 used for paper bleaching.
  Acta Crystallogr D Biol Crystallogr, 59, 627-636.
PDB code: 1igo
12653995 N.Hakulinen, O.Turunen, J.Jänis, M.Leisola, and J.Rouvinen (2003).
Three-dimensional structures of thermophilic beta-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa. Comparison of twelve xylanases in relation to their thermal stability.
  Eur J Biochem, 270, 1399-1412.
PDB codes: 1h1a 1m4w
12492845 B.Rotblat, D.Enshell-Seijffers, J.M.Gershoni, S.Schuster, and A.Avni (2002).
Identification of an essential component of the elicitation active site of the EIX protein elicitor.
  Plant J, 32, 1049-1055.  
12146939 D.J.Vocadlo, J.Wicki, K.Rupitz, and S.G.Withers (2002).
A case for reverse protonation: identification of Glu160 as an acid/base catalyst in Thermoanaerobacterium saccharolyticum beta-xylosidase and detailed kinetic analysis of a site-directed mutant.
  Biochemistry, 41, 9736-9746.  
12207016 T.A.Tahir, J.G.Berrin, R.Flatman, A.Roussel, P.Roepstorff, G.Williamson, and N.Juge (2002).
Specific characterization of substrate and inhibitor binding sites of a glycosyl hydrolase family 11 xylanase from Aspergillus niger.
  J Biol Chem, 277, 44035-44043.  
11717493 J.Wouters, J.Georis, D.Engher, J.Vandenhaute, J.Dusart, J.M.Frere, E.Depiereux, and P.Charlier (2001).
Crystallographic analysis of family 11 endo-beta-1,4-xylanase Xyl1 from Streptomyces sp. S38.
  Acta Crystallogr D Biol Crystallogr, 57, 1813-1819.
PDB code: 1hix
11053833 A.A.McCarthy, D.D.Morris, P.L.Bergquist, and E.N.Baker (2000).
Structure of XynB, a highly thermostable beta-1,4-xylanase from Dictyoglomus thermophilum Rt46B.1, at 1.8 A resolution.
  Acta Crystallogr D Biol Crystallogr, 56, 1367-1375.
PDB code: 1f5j
  10752613 G.P.Connelly, S.G.Withers, and L.P.McIntosh (2000).
Analysis of the dynamic properties of Bacillus circulans xylanase upon formation of a covalent glycosyl-enzyme intermediate.
  Protein Sci, 9, 512-524.  
  10752608 J.Georis, F.de Lemos Esteves, J.Lamotte-Brasseur, V.Bougnet, B.Devreese, F.Giannotta, B.Granier, and J.M.Frère (2000).
An additional aromatic interaction improves the thermostability and thermophilicity of a mesophilic family 11 xylanase: structural basis and molecular study.
  Protein Sci, 9, 466-475.  
11210125 J.X.Feng, S.Karita, E.Fujino, T.Fujino, T.Kimura, K.Sakka, and K.Ohmiya (2000).
Cloning, sequencing, and expression of the gene encoding a cell-bound multi-domain xylanase from Clostridium josui, and characterization of the translated product.
  Biosci Biotechnol Biochem, 64, 2614-2624.  
11210150 T.Kimura, H.Suzuki, H.Furuhashi, T.Aburatani, K.Morimoto, S.Karita, K.Sakka, and K.Ohmiya (2000).
Molecular cloning, overexpression, and purification of a major xylanase from Aspergillus oryzae.
  Biosci Biotechnol Biochem, 64, 2734-2738.  
10923795 T.Kimura, J.Ito, A.Kawano, T.Makino, H.Kondo, S.Karita, K.Sakka, and K.Ohmiya (2000).
Purification, characterization, and molecular cloning of acidophilic xylanase from penicillium sp.40.
  Biosci Biotechnol Biochem, 64, 1230-1237.  
10446364 I.Connerton, N.Cummings, G.W.Harris, P.Debeire, and C.Breton (1999).
A single domain thermophilic xylanase can bind insoluble xylan: evidence for surface aromatic clusters.
  Biochim Biophys Acta, 1433, 110-121.  
  9209040 H.Hayashi, K.I.Takagi, M.Fukumura, T.Kimura, S.Karita, K.Sakka, and K.Ohmiya (1997).
Sequence of xynC and properties of XynC, a major component of the Clostridium thermocellum cellulosome.
  J Bacteriol, 179, 4246-4253.  
  9416621 M.D.Joshi, A.Hedberg, and L.P.McIntosh (1997).
Complete measurement of the pKa values of the carboxyl and imidazole groups in Bacillus circulans xylanase.
  Protein Sci, 6, 2667-2670.  
18576090 M.E.Himmel, P.A.Karplus, J.Sakon, W.S.Adney, J.O.Baker, and S.R.Thomas (1997).
Polysaccharide hydrolase folds diversity of structure and convergence of function.
  Appl Biochem Biotechnol, 63, 315-325.  
  8931150 L.A.Plesniak, G.P.Connelly, W.W.Wakarchuk, and L.P.McIntosh (1996).
Characterization of a buried neutral histidine residue in Bacillus circulans xylanase: NMR assignments, pH titration, and hydrogen exchange.
  Protein Sci, 5, 2319-2328.  
  8762143 L.A.Plesniak, W.W.Wakarchuk, and L.P.McIntosh (1996).
Secondary structure and NMR assignments of Bacillus circulans xylanase.
  Protein Sci, 5, 1118-1135.  
8810338 S.Zeilinger, R.L.Mach, M.Schindler, P.Herzog, and C.P.Kubicek (1996).
Different inducibility of expression of the two xylanase genes xyn1 and xyn2 in Trichoderma reesei.
  J Biol Chem, 271, 25624-25629.  
8785441 T.W.Jeffries (1996).
Biochemistry and genetics of microbial xylanases.
  Curr Opin Biotechnol, 7, 337-342.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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