PDBsum entry 1ukr

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Hydrolase PDB id
Protein chains
181 a.a. *
Waters ×288
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of endo-1,4-beta-xylanasE C
Structure: Endo-1,4-b-xylanase i. Chain: a, b, c, d. Synonym: xylanase. Engineered: yes
Source: Aspergillus niger. Organism_taxid: 5061. Expressed in: escherichia coli. Expression_system_taxid: 562
2.40Å     R-factor:   0.179    
Authors: U.Krengel,B.W.Dijkstra
Key ref:
U.Krengel and B.W.Dijkstra (1996). Three-dimensional structure of Endo-1,4-beta-xylanase I from Aspergillus niger: molecular basis for its low pH optimum. J Mol Biol, 263, 70-78. PubMed id: 8890913 DOI: 10.1006/jmbi.1996.0556
23-Aug-96     Release date:   24-Dec-97    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P55329  (XYNA_ASPNG) -  Endo-1,4-beta-xylanase A
211 a.a.
181 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - 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!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  


DOI no: 10.1006/jmbi.1996.0556 J Mol Biol 263:70-78 (1996)
PubMed id: 8890913  
Three-dimensional structure of Endo-1,4-beta-xylanase I from Aspergillus niger: molecular basis for its low pH optimum.
U.Krengel, B.W.Dijkstra.
The crystal structure of endo-1,4-beta-xylanase I from Aspergillus niger has been solved by molecular replacement and was refined to 2.4 A resolution. The final R-factor for all data from 6 to 2.4 A is 17.9%. The A. niger xylanase has a characteristic fold which is unique for family G xylanases (root-mean-square deviation = 1.1 A to Trichoderma reesei xylanase I, which has 53% sequence identity). It consists of a single domain composed predominantly of beta-strands. Two beta-sheets are twisted around a deep, long cleft, which is lined with many aromatic amino acid residues and is large enough to accommodate at least four xylose residues. The two conserved glutamate residues, Glu79 and Glu170, which are likely to be involved in catalysis, reach into this cleft from opposite sides. A niger xylanase I is of particular commercial interest because of its low pH optimum. A model is proposed which explains this low pH optimum compared to other members of xylanase family G.
  Selected figure(s)  
Figure 1.
Figure 1. Representative part of the sA-weighted (Read, 1986) (2 Fo - Fc) OMIT map (Bhat, 1988), centered at Ile82 and contoured at 1s.
Figure 5.
Figure 5. Sketch of the interactions in the active site of A. niger xylanase I.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 263, 70-78) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20593181 J.Xie, L.Song, X.Li, X.Yi, H.Xu, J.Li, D.Qiao, and Y.Cao (2011).
Site-directed mutagenesis and thermostability of xylanase XYNB from Aspergillus niger 400264.
  Curr Microbiol, 62, 242-248.  
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.  
19626289 W.Liu, P.Shi, Q.Chen, P.Yang, G.Wang, Y.Wang, H.Luo, and B.Yao (2010).
Gene cloning, overexpression, and characterization of a xylanase from Penicillium sp. CGMCC 1669.
  Appl Biochem Biotechnol, 162, 1.  
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.  
17729269 A.May, and M.Zacharias (2008).
Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking.
  Proteins, 70, 794-809.  
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.  
18157528 Y.H.Liu, F.P.Lu, Y.Li, X.B.Yin, Y.Wang, and C.Gao (2008).
Characterisation of mutagenised acid-resistant alpha-amylase expressed in Bacillus subtilis WB600.
  Appl Microbiol Biotechnol, 78, 85-94.  
17691895 B.Y.Chen, V.Y.Fofanov, D.H.Bryant, B.D.Dodson, D.M.Kristensen, A.M.Lisewski, M.Kimmel, O.Lichtarge, and L.E.Kavraki (2007).
The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs.
  J Comput Biol, 14, 791-816.  
16428847 B.Al Balaa, J.Wouters, S.Dogne, C.Rossini, J.M.Schaus, E.Depiereux, J.Vandenhaute, and I.Housen (2006).
Identification, cloning, and expression of the Scytalidium acidophilum XYL1 gene encoding for an acidophilic xylanase.
  Biosci Biotechnol Biochem, 70, 269-272.  
16652352 M.Kozak (2006).
Solution scattering studies of conformation stability of xylanase XYNII from Trichoderma longibrachiatum.
  Biopolymers, 83, 95.  
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
15981255 C.Zhang, S.Liu, and Y.Zhou (2005).
Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function.
  Proteins, 60, 314-318.  
15981268 E.Ben-Zeev, N.Kowalsman, A.Ben-Shimon, D.Segal, T.Atarot, O.Noivirt, T.Shay, and M.Eisenstein (2005).
Docking to single-domain and multiple-domain proteins: old and new challenges.
  Proteins, 60, 195-201.  
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.  
16279951 K.Fierens, A.Gils, S.Sansen, K.Brijs, C.M.Courtin, P.J.Declerck, C.J.De Ranter, K.Gebruers, A.Rabijns, J.Robben, S.Campenhout, G.Volckaert, and J.A.Delcour (2005).
His374 of wheat endoxylanase inhibitor TAXI-I stabilizes complex formation with glycoside hydrolase family 11 endoxylanases.
  FEBS J, 272, 5872-5882.  
15981263 K.Wiehe, B.Pierce, J.Mintseris, W.W.Tong, R.Anderson, R.Chen, and Z.Weng (2005).
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5.
  Proteins, 60, 207-213.  
  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.  
15981270 M.Zacharias (2005).
ATTRACT: protein-protein docking in CAPRI using a reduced protein model.
  Proteins, 60, 252-256.  
15652973 T.Collins, C.Gerday, and G.Feller (2005).
Xylanases, xylanase families and extremophilic xylanases.
  FEMS Microbiol Rev, 29, 3.  
16086105 X.Y.Weng, and J.Y.Sun (2005).
Construction, expression, and characterization of a thermostable xylanase.
  Curr Microbiol, 51, 188-192.  
15981251 Y.Inbar, D.Schneidman-Duhovny, I.Halperin, A.Oron, R.Nussinov, and H.J.Wolfson (2005).
Approaching the CAPRI challenge with an efficient geometry-based docking.
  Proteins, 60, 217-223.  
15181003 F.Payan, P.Leone, S.Porciero, C.Furniss, T.Tahir, G.Williamson, A.Durand, P.Manzanares, H.J.Gilbert, N.Juge, and A.Roussel (2004).
The dual nature of the wheat xylanase protein inhibitor XIP-I: structural basis for the inhibition of family 10 and family 11 xylanases.
  J Biol Chem, 279, 36029-36037.
PDB codes: 1ta3 1te1
15096627 Lemos Esteves, V.Ruelle, J.Lamotte-Brasseur, B.Quinting, and J.M.Frère (2004).
Acidophilic adaptation of family 11 endo-beta-1,4-xylanases: modeling and mutational analysis.
  Protein Sci, 13, 1209-1218.  
  16233716 H.Tanaka, T.Okuno, S.Moriyama, M.Muguruma, and K.Ohta (2004).
Acidophilic xylanase from Aureobasidium pullulans: efficient expression and secretion in Pichia pastoris and mutational analysis.
  J Biosci Bioeng, 98, 338-343.  
15278768 H.Xiong, F.Fenel, M.Leisola, and O.Turunen (2004).
Engineering the thermostability of Trichoderma reesei endo-1,4-beta-xylanase II by combination of disulphide bridges.
  Extremophiles, 8, 393-400.  
15557263 M.Strohmeier, M.Hrmova, M.Fischer, A.J.Harvey, G.B.Fincher, and J.Pleiss (2004).
Molecular modeling of family GH16 glycoside hydrolases: potential roles for xyloglucan transglucosylases/hydrolases in cell wall modification in the poaceae.
  Protein Sci, 13, 3200-3213.  
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.  
14993691 S.Sansen, C.J.De Ranter, K.Gebruers, K.Brijs, C.M.Courtin, J.A.Delcour, and A.Rabijns (2004).
Crystallization and preliminary X-ray diffraction study of two complexes of a TAXI-type xylanase inhibitor with glycoside hydrolase family 11 xylanases from Aspergillus niger and Bacillus subtilis.
  Acta Crystallogr D Biol Crystallogr, 60, 555-557.  
15166216 S.Sansen, C.J.De Ranter, K.Gebruers, K.Brijs, C.M.Courtin, J.A.Delcour, and A.Rabijns (2004).
Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I.
  J Biol Chem, 279, 36022-36028.
PDB codes: 1t6e 1t6g
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.  
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
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.  
11846790 E.Bokma, H.J.Rozeboom, M.Sibbald, B.W.Dijkstra, and J.J.Beintema (2002).
Expression and characterization of active site mutants of hevamine, a chitinase from the rubber tree Hevea brasiliensis.
  Eur J Biochem, 269, 893-901.
PDB codes: 1kqy 1kqz 1kr0 1kr1
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
16233094 K.Ohta, S.Moriyama, H.Tanaka, T.Shige, and H.Akimoto (2001).
Purification and characterization of an acidophilic xylanase from Aureobasidium pullulans var. melanigenum and sequence analysis of the encoding gene.
  J Biosci Bioeng, 92, 262-270.  
11729262 Vries, and J.Visser (2001).
Aspergillus enzymes involved in degradation of plant cell wall polysaccharides.
  Microbiol Mol Biol Rev, 65, 497.  
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.  
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.  
10491128 J.E.Nielsen, L.Beier, D.Otzen, T.V.Borchert, H.B.Frantzen, K.V.Andersen, and A.Svendsen (1999).
Electrostatics in the active site of an alpha-amylase.
  Eur J Biochem, 264, 816-824.  
10422261 N.Kulkarni, A.Shendye, and M.Rao (1999).
Molecular and biotechnological aspects of xylanases.
  FEMS Microbiol Rev, 23, 411-456.  
  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.  
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 codes are shown on the right.