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PDBsum entry 1bcx

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Hydrolase(xylan degradation) PDB id
1bcx
Jmol
Contents
Protein chain
185 a.a. *
Ligands
XYP-XYP
SO4
Waters ×144
* Residue conservation analysis
PDB id:
1bcx
Name: Hydrolase(xylan degradation)
Title: Mutational and crystallographic analyses of the active site residues of the bacillus circulans xylanase
Structure: Xylanase. Chain: a. Engineered: yes
Source: Bacillus circulans. Organism_taxid: 1397
Resolution:
1.81Å     R-factor:   0.161    
Authors: R.L.Campbell,W.W.Wakarchuk
Key ref:
W.W.Wakarchuk et al. (1994). Mutational and crystallographic analyses of the active site residues of the Bacillus circulans xylanase. Protein Sci, 3, 467-475. PubMed id: 8019418 DOI: 10.1002/pro.5560030312
Date:
01-Apr-94     Release date:   15-Oct-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P09850  (XYNA_BACCI) -  Endo-1,4-beta-xylanase
Seq:
Struc:
213 a.a.
185 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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: 10.1002/pro.5560030312 Protein Sci 3:467-475 (1994)
PubMed id: 8019418  
 
 
Mutational and crystallographic analyses of the active site residues of the Bacillus circulans xylanase.
W.W.Wakarchuk, R.L.Campbell, W.L.Sung, J.Davoodi, M.Yaguchi.
 
  ABSTRACT  
 
Using site-directed mutagenesis we have investigated the catalytic residues in a xylanase from Bacillus circulans. Analysis of the mutants E78D and E172D indicated that mutations in these conserved residues do not grossly alter the structure of the enzyme and that these residues participate in the catalytic mechanism. We have now determined the crystal structure of an enzyme-substrate complex to 108 A resolution using a catalytically incompetent mutant (E172C). In addition to the catalytic residues, Glu 78 and Glu 172, we have identified 2 tyrosine residues, Tyr 69 and Tyr 80, which likely function in substrate binding, and an arginine residue, Arg 112, which plays an important role in the active site of this enzyme. On the basis of our work we would propose that Glu 78 is the nucleophile and that Glu 172 is the acid-base catalyst in the reaction.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. General reaction mechanism fora retaining endo-0-D-xylanase. The structures of thesubstrate, intermediates, and product have been simplified for clarity. R = xyl(,,), HA the acid catalyst, I = the struc- ures he brackets are possible intermediates, and R, = H or xyl(,,). The reaction proceeds by adouble mechanism general acid catalysis/nucleophilic attack on theanomeric produces 1 of 2 intermediates. Intermediate (a) has acar- boxylate acting in an ion pair to stabilize an oxo-carbonium ion, hereas ntermediate(b) shows hat thetransitionstate has collapsed intoaco- glycosyl-enzyme. Either of these intermediates could then react with a nucleophilic water (R, = H) to produce hydrolysis products or another xylo-oligosaccharide (R, = to produce trans-glycosy- ation products. The transition states for both steps are likely to have sub- stantialoxo-carboniumioncharacter.
Figure 4.
Fig. 4. CD spectra of selectdactivesitemutants of the B. circulans xy- lanase. Thewild-typeenzymespectrumis shown bythe solid line, the E78D mutantspectrumis shown bythe - - - line, and the spec- trumis shown by the mixed line.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1994, 3, 467-475) copyright 1994.  
  Figures were selected by an automated process.  

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.
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Molecular cloning and characterization of a bifunctional xylanolytic enzyme from Neocallimastix patriciarum.
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20072608 N.Todaka, T.Inoue, K.Saita, M.Ohkuma, C.A.Nalepa, M.Lenz, T.Kudo, and S.Moriya (2010).
Phylogenetic analysis of cellulolytic enzyme genes from representative lineages of termites and a related cockroach.
  PLoS One, 5, e8636.  
19940147 O.Gallardo, F.I.Pastor, J.Polaina, P.Diaz, R.Łysek, P.Vogel, P.Isorna, B.González, and J.Sanz-Aparicio (2010).
Structural insights into the specificity of Xyn10B from Paenibacillus barcinonensis and its improved stability by forced protein evolution.
  J Biol Chem, 285, 2721-2733.
PDB codes: 3emc 3emq 3emz
20538726 T.C.Freeman, and W.C.Wimley (2010).
A highly accurate statistical approach for the prediction of transmembrane beta-barrels.
  Bioinformatics, 26, 1965-1974.  
18953653 A.Kumar, N.K.Singhal, B.Ramanujam, A.Mitra, N.R.Rameshwaram, S.K.Nadimpalli, and C.P.Rao (2009).
C(1)-/C(2)-aromatic-imino-glyco-conjugates: experimental and computational studies of binding, inhibition and docking aspects towards glycosidases isolated from soybean and jack bean.
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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
19788271 L.M.Willis, R.Zhang, A.Reid, S.G.Withers, and W.W.Wakarchuk (2009).
Mechanistic investigation of the endo-alpha-N-acetylgalactosaminidase from Streptococcus pneumoniae R6.
  Biochemistry, 48, 10334-10341.  
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.  
18491328 D.J.Namdjou, H.M.Chen, E.Vinogradov, D.Brochu, S.G.Withers, and W.W.Wakarchuk (2008).
A beta-1,4-galactosyltransferase from Helicobacter pylori is an efficient and versatile biocatalyst displaying a novel activity for thioglycoside synthesis.
  Chembiochem, 9, 1632-1640.  
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.  
17952884 O.Hekmat, C.Florizone, Y.W.Kim, L.D.Eltis, R.A.Warren, and S.G.Withers (2007).
Specificity fingerprinting of retaining beta-1,4-glycanases in the Cellulomonas fimi secretome using two fluorescent mechanism-based probes.
  Chembiochem, 8, 2125-2132.  
16528765 J.Müllegger, H.M.Chen, R.A.Warren, and S.G.Withers (2006).
Glycosylation of a neoglycoprotein by using glycosynthase and thioglycoligase approaches: the generation of a thioglycoprotein.
  Angew Chem Int Ed Engl, 45, 2585-2588.  
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
16397879 S.J.Williams, O.Hekmat, and S.G.Withers (2006).
Synthesis and testing of mechanism-based protein-profiling probes for retaining endo-glycosidases.
  Chembiochem, 7, 116-124.  
15659364 F.De Lemos Esteves, T.Gouders, J.Lamotte-Brasseur, S.Rigali, and J.M.Frère (2005).
Improving the alkalophilic performances of the Xyl1 xylanase from Streptomyces sp. S38: structural comparison and mutational analysis.
  Protein Sci, 14, 292-302.  
15965663 J.Beaugrand, G.Paës, D.Reis, M.Takahashi, P.Debeire, M.O'donohue, and B.Chabbert (2005).
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  Planta, 222, 246-257.  
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
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.  
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.  
15096627 F.de 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.  
14718652 N.Palackal, Y.Brennan, W.N.Callen, P.Dupree, G.Frey, F.Goubet, G.P.Hazlewood, S.Healey, Y.E.Kang, K.A.Kretz, E.Lee, X.Tan, G.L.Tomlinson, J.Verruto, V.W.Wong, E.J.Mathur, J.M.Short, D.E.Robertson, and B.A.Steer (2004).
An evolutionary route to xylanase process fitness.
  Protein Sci, 13, 494-503.  
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.  
15184164 Y.Brennan, W.N.Callen, L.Christoffersen, P.Dupree, F.Goubet, S.Healey, M.Hernández, M.Keller, K.Li, N.Palackal, A.Sittenfeld, G.Tamayo, S.Wells, G.P.Hazlewood, E.J.Mathur, J.M.Short, D.E.Robertson, and B.A.Steer (2004).
Unusual microbial xylanases from insect guts.
  Appl Environ Microbiol, 70, 3609-3617.  
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
12930989 J.E.Nielsen, and J.A.McCammon (2003).
Calculating pKa values in enzyme active sites.
  Protein Sci, 12, 1894-1901.  
14517232 K.Hövel, D.Shallom, K.Niefind, V.Belakhov, G.Shoham, T.Baasov, Y.Shoham, and D.Schomburg (2003).
Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase.
  EMBO J, 22, 4922-4932.
PDB codes: 1pz2 1pz3 1qw8 1qw9
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
11222610 J.C.Hurlbert, and J.F.Preston (2001).
Functional characterization of a novel xylanase from a corn strain of Erwinia chrysanthemi.
  J Bacteriol, 183, 2093-2100.  
11340657 J.E.Nielsen, and G.Vriend (2001).
Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations.
  Proteins, 43, 403-412.  
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.  
11025547 L.L.Leggio, J.Jenkins, G.W.Harris, and R.W.Pickersgill (2000).
X-ray crystallographic study of xylopentaose binding to Pseudomonas fluorescens xylanase A.
  Proteins, 41, 362-373.
PDB code: 1e5n
10995222 V.Notenboom, S.J.Williams, R.Hoos, S.G.Withers, and D.R.Rose (2000).
Detailed structural analysis of glycosidase/inhibitor interactions: complexes of Cex from Cellulomonas fimi with xylobiose-derived aza-sugars.
  Biochemistry, 39, 11553-11563.
PDB codes: 1fh7 1fh8 1fh9 1fhd
10220321 G.Sidhu, S.G.Withers, N.T.Nguyen, L.P.McIntosh, L.Ziser, and G.D.Brayer (1999).
Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.
  Biochemistry, 38, 5346-5354.
PDB codes: 1bvv 2bvv
10200171 G.Sulzenbacher, L.F.Mackenzie, K.S.Wilson, S.G.Withers, C.Dupont, and G.J.Davies (1999).
The crystal structure of a 2-fluorocellotriosyl complex of the Streptomyces lividans endoglucanase CelB2 at 1.2 A resolution.
  Biochemistry, 38, 4826-4833.
PDB code: 2nlr
10872458 H.D.Ly, and S.G.Withers (1999).
Mutagenesis of glycosidases.
  Annu Rev Biochem, 68, 487-522.  
10422261 N.Kulkarni, A.Shendye, and M.Rao (1999).
Molecular and biotechnological aspects of xylanases.
  FEMS Microbiol Rev, 23, 411-456.  
9601025 D.L.Zechel, L.Konermann, S.G.Withers, and D.J.Douglas (1998).
Pre-steady state kinetic analysis of an enzymatic reaction monitored by time-resolved electrospray ionization mass spectrometry.
  Biochemistry, 37, 7664-7669.  
9485306 G.P.Connelly, and L.P.McIntosh (1998).
Characterization of a buried neutral histidine in Bacillus circulans xylanase: internal dynamics and interaction with a bound water molecule.
  Biochemistry, 37, 1810-1818.  
9521693 H.P.Fierobe, E.Mirgorodskaya, K.A.McGuire, P.Roepstorff, B.Svensson, and A.J.Clarke (1998).
Restoration of catalytic activity beyond wild-type level in glucoamylase from Aspergillus awamori by oxidation of the Glu400-->Cys catalytic-base mutant to cysteinesulfinic acid.
  Biochemistry, 37, 3743-3752.  
9618460 J.Aÿ, F.Götz, R.Borriss, and U.Heinemann (1998).
Structure and function of the Bacillus hybrid enzyme GluXyn-1: native-like jellyroll fold preserved after insertion of autonomous globular domain.
  Proc Natl Acad Sci U S A, 95, 6613-6618.
PDB code: 1axk
  9684886 J.Davoodi, W.W.Wakarchuk, W.K.Surewicz, and P.R.Carey (1998).
Scan-rate dependence in protein calorimetry: the reversible transitions of Bacillus circulans xylanase and a disulfide-bridge mutant.
  Protein Sci, 7, 1538-1544.  
9753433 K.Gruber, G.Klintschar, M.Hayn, A.Schlacher, W.Steiner, and C.Kratky (1998).
Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies.
  Biochemistry, 37, 13475-13485.
PDB code: 1yna
9374861 C.Malet, and A.Planas (1997).
Mechanism of Bacillus 1,3-1,4-beta-D-glucan 4-glucanohydrolases: kinetics and pH studies with 4-methylumbelliferyl beta-D-glucan oligosaccharides.
  Biochemistry, 36, 13838-13848.  
  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.  
9363771 M.Gilbert, A.M.Cunningham, D.C.Watson, A.Martin, J.C.Richards, and W.W.Wakarchuk (1997).
Characterization of a recombinant Neisseria meningitidis alpha-2,3-sialyltransferase and its acceptor specificity.
  Eur J Biochem, 249, 187-194.  
9047328 S.L.Lawson, W.W.Wakarchuk, and S.G.Withers (1997).
Positioning the acid/base catalyst in a glycosidase: studies with Bacillus circulans xylanase.
  Biochemistry, 36, 2257-2265.  
8855954 A.M.MacLeod, D.Tull, K.Rupitz, R.A.Warren, and S.G.Withers (1996).
Mechanistic consequences of mutation of active site carboxylates in a retaining beta-1,4-glycanase from Cellulomonas fimi.
  Biochemistry, 35, 13165-13172.  
  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.  
8756457 L.P.McIntosh, G.Hand, P.E.Johnson, M.D.Joshi, M.Körner, L.A.Plesniak, L.Ziser, W.W.Wakarchuk, and S.G.Withers (1996).
The pKa of the general acid/base carboxyl group of a glycosidase cycles during catalysis: a 13C-NMR study of bacillus circulans xylanase.
  Biochemistry, 35, 9958-9966.  
8755744 R.Havukainen, A.Törrönen, T.Laitinen, and J.Rouvinen (1996).
Covalent binding of three epoxyalkyl xylosides to the active site of endo-1,4-xylanase II from Trichoderma reesei.
  Biochemistry, 35, 9617-9624.
PDB codes: 1red 1ree 1ref
8756474 S.L.Lawson, W.W.Wakarchuk, and S.G.Withers (1996).
Effects of both shortening and lengthening the active site nucleophile of Bacillus circulans xylanase on catalytic activity.
  Biochemistry, 35, 10110-10118.  
  8845760 X.Chen, D.Whitmire, and J.P.Bowen (1996).
Xylanase homology modeling using the inverse protein folding approach.
  Protein Sci, 5, 705-708.  
  8528065 G.Kreil (1995).
Hyaluronidases--a group of neglected enzymes.
  Protein Sci, 4, 1666-1669.  
  7588724 J.Davoodi, W.W.Wakarchuk, R.L.Campbell, P.R.Carey, and W.K.Surewicz (1995).
Abnormally high pKa of an active-site glutamic acid residue in Bacillus circulans xylanase. The role of electrostatic interactions.
  Eur J Biochem, 232, 839-843.  
  7795519 S.G.Withers, and R.Aebersold (1995).
Approaches to labeling and identification of active site residues in glycosidases.
  Protein Sci, 4, 361-372.  
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.