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PDBsum entry 2bvv

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protein links
Hydrolase PDB id
2bvv
Jmol
Contents
Protein chain
185 a.a. *
Waters ×148
* Residue conservation analysis
PDB id:
2bvv
Name: Hydrolase
Title: Sugar ring distortion in the glycosyl-enzyme intermediate of a family g/11 xylanase.
Structure: Protein (endo-1,4-beta-xylanase). Chain: a. Synonym: bcx. Engineered: yes. Mutation: yes
Source: Bacillus circulans. Organism_taxid: 1397. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.50Å     R-factor:   0.188    
Authors: G.Sidhu,G.D.Brayer
Key ref:
G.Sidhu et al. (1999). Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase. Biochemistry, 38, 5346-5354. PubMed id: 10220321 DOI: 10.1021/bi982946f
Date:
17-Nov-98     Release date:   02-Jun-99    
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: 10.1021/bi982946f Biochemistry 38:5346-5354 (1999)
PubMed id: 10220321  
 
 
Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.
G.Sidhu, S.G.Withers, N.T.Nguyen, L.P.McIntosh, L.Ziser, G.D.Brayer.
 
  ABSTRACT  
 
The 1.8 A resolution structure of the glycosyl-enzyme intermediate formed on the retaining beta-1,4-xylanase from Bacillus circulans has been determined using X-ray crystallographic techniques. The 2-fluoro-xylose residue bound in the -1 subsite adopts a 2,5B (boat) conformation, allowing atoms C5, O5, C1, and C2 of the sugar to achieve coplanarity as required at the oxocarbenium ion-like transition states of the double-displacement catalytic mechanism. Comparison of this structure to that of a mutant of this same enzyme noncovalently complexed with xylotetraose [Wakarchuk et al. (1994) Protein Sci. 3, 467-475] reveals a number of differences beyond the distortion of the sugar moiety. Most notably, a bifurcated hydrogen bond interaction is formed in the glycosyl-enzyme intermediate involving Heta of Tyr69, the endocyclic oxygen (O5) of the xylose residue in the -1 subsite, and Oepsilon2 of the catalytic nucleophile, Glu78. To gain additional understanding of the role of Tyr69 at the active site of this enzyme, we also determined the 1.5 A resolution structure of the catalytically inactive Tyr69Phe mutant. Interestingly, no significant structural perturbation due to the loss of the phenolic group is observed. These results suggest that the interactions involving the phenolic group of Tyr69, O5 of the proximal saccharide, and Glu78 Oepsilon2 are important for the catalytic mechanism of this enzyme, and it is proposed that, through charge redistribution, these interactions serve to stabilize the oxocarbenium-like ion of the transition state. Studies of the covalent glycosyl-enzyme intermediate of this xylanase also provide insight into specificity, as contacts with C5 of the xylose moiety exclude sugars with hydroxymethyl substituents, and the mechanism of catalysis, including aspects of stereoelectronic theory as applied to glycoside hydrolysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20127424 D.B.Jordan, and J.D.Braker (2010).
beta-D-Xylosidase from Selenomonas ruminantium: role of glutamate 186 in catalysis revealed by site-directed mutagenesis, alternate substrates, and active-site inhibitor.
  Appl Biochem Biotechnol, 161, 395-410.  
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
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
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.  
19279191 R.Suzuki, Z.Fujimoto, S.Ito, S.Kawahara, S.Kaneko, K.Taira, T.Hasegawa, and A.Kuno (2009).
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.
  J Biochem, 146, 61-70.
PDB codes: 2d1z 2d20 2d22 2d23 2d24
18498103 D.C.Bas, D.M.Rogers, and J.H.Jensen (2008).
Very fast prediction and rationalization of pKa values for protein-ligand complexes.
  Proteins, 73, 765-783.  
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.  
18808119 P.A.Sigala, D.A.Kraut, J.M.Caaveiro, B.Pybus, E.A.Ruben, D.Ringe, G.A.Petsko, and D.Herschlag (2008).
Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.
  J Am Chem Soc, 130, 13696-13708.
PDB codes: 2inx 3cpo
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.  
18499583 T.Parkkinen, A.Koivula, J.Vehmaanperä, and J.Rouvinen (2008).
Crystal structures of Melanocarpus albomyces cellobiohydrolase Cel7B in complex with cello-oligomers show high flexibility in the substrate binding.
  Protein Sci, 17, 1383-1394.
PDB codes: 2rfw 2rfy 2rfz 2rg0
17892319 C.Chennubhotla, and I.Bahar (2007).
Signal propagation in proteins and relation to equilibrium fluctuations.
  PLoS Comput Biol, 3, 1716-1726.  
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
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).
Probing the cell wall heterogeneity of micro-dissected wheat caryopsis using both active and inactive forms of a GH11 xylanase.
  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
15939021 L.W.Yang, and I.Bahar (2005).
Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes.
  Structure, 13, 893-904.  
14638688 A.Hirata, M.Adachi, A.Sekine, Y.N.Kang, S.Utsumi, and B.Mikami (2004).
Structural and enzymatic analysis of soybean beta-amylase mutants with increased pH optimum.
  J Biol Chem, 279, 7287-7295.
PDB codes: 1q6c 1q6d 1q6e 1q6f 1q6g
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
15515081 F.Vincent, T.M.Gloster, J.Macdonald, C.Morland, R.V.Stick, F.M.Dias, J.A.Prates, C.M.Fontes, H.J.Gilbert, and G.J.Davies (2004).
Common inhibition of both beta-glucosidases and beta-mannosidases by isofagomine lactam reflects different conformational itineraries for pyranoside hydrolysis.
  Chembiochem, 5, 1596-1599.
PDB codes: 1uz1 1uz4
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.  
14573597 G.Golan, D.Shallom, A.Teplitsky, G.Zaide, S.Shulami, T.Baasov, V.Stojanoff, A.Thompson, Y.Shoham, and G.Shoham (2004).
Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications.
  J Biol Chem, 279, 3014-3024.
PDB codes: 1k9d 1k9e 1k9f 1l8n 1mqp 1mqq 1mqr
14668328 G.Pell, E.J.Taylor, T.M.Gloster, J.P.Turkenburg, C.M.Fontes, L.M.Ferreira, T.Nagy, S.J.Clark, G.J.Davies, and H.J.Gilbert (2004).
The mechanisms by which family 10 glycoside hydrolases bind decorated substrates.
  J Biol Chem, 279, 9597-9605.
PDB codes: 1uqy 1uqz 1ur1 1ur2
14997537 J.K.Choi, B.H.Lee, C.H.Chae, and W.Shin (2004).
Computer modeling of the rhamnogalacturonase-"hairy" pectin complex.
  Proteins, 55, 22-33.  
14597633 M.Hrmova, R.De Gori, B.J.Smith, A.Vasella, J.N.Varghese, and G.B.Fincher (2004).
Three-dimensional structure of the barley beta-D-glucan glucohydrolase in complex with a transition state mimic.
  J Biol Chem, 279, 4970-4980.
PDB code: 1lq2
15356002 T.M.Gloster, J.M.Macdonald, C.A.Tarling, R.V.Stick, S.G.Withers, and G.J.Davies (2004).
Structural, thermodynamic, and kinetic analyses of tetrahydrooxazine-derived inhibitors bound to beta-glucosidases.
  J Biol Chem, 279, 49236-49242.
PDB codes: 1w3j 1w3k 1w3l
15252054 Y.W.Kim, S.S.Lee, R.A.Warren, and S.G.Withers (2004).
Directed evolution of a glycosynthase from Agrobacterium sp. increases its catalytic activity dramatically and expands its substrate repertoire.
  J Biol Chem, 279, 42787-42793.  
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
12595701 A.Varrot, and G.J.Davies (2003).
Direct experimental observation of the hydrogen-bonding network of a glycosidase along its reaction coordinate revealed by atomic resolution analyses of endoglucanase Cel5A.
  Acta Crystallogr D Biol Crystallogr, 59, 447-452.
PDB codes: 1h11 1h2j 1hf6
12704087 D.A.Kraut, K.S.Carroll, and D.Herschlag (2003).
Challenges in enzyme mechanism and energetics.
  Annu Rev Biochem, 72, 517-571.  
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
12960159 S.Numao, D.A.Kuntz, S.G.Withers, and D.R.Rose (2003).
Insights into the mechanism of Drosophila melanogaster Golgi alpha-mannosidase II through the structural analysis of covalent reaction intermediates.
  J Biol Chem, 278, 48074-48083.
PDB codes: 1qwn 1qwu 1qx1
12454501 A.Varrot, T.P.Frandsen, H.Driguez, and G.J.Davies (2002).
Structure of the Humicola insolens cellobiohydrolase Cel6A D416A mutant in complex with a non-hydrolysable substrate analogue, methyl cellobiosyl-4-thio-beta-cellobioside, at 1.9 A.
  Acta Crystallogr D Biol Crystallogr, 58, 2201-2204.
PDB code: 1gz1
12413546 A.Vasella, G.J.Davies, and M.Böhm (2002).
Glycosidase mechanisms.
  Curr Opin Chem Biol, 6, 619-629.  
12146938 D.J.Vocadlo, J.Wicki, K.Rupitz, and S.G.Withers (2002).
Mechanism of Thermoanaerobacterium saccharolyticum beta-xylosidase: kinetic studies.
  Biochemistry, 41, 9727-9735.  
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.  
11900558 T.Kaper, H.H.van Heusden, B.van Loo, A.Vasella, J.van der Oost, and W.M.de Vos (2002).
Substrate specificity engineering of beta-mannosidase and beta-glucosidase from Pyrococcus by exchange of unique active site residues.
  Biochemistry, 41, 4147-4155.  
11526340 E.Sabini, K.S.Wilson, S.Danielsen, M.Schülein, and G.J.Davies (2001).
Oligosaccharide binding to family 11 xylanases: both covalent intermediate and mutant product complexes display (2,5)B conformations at the active centre.
  Acta Crystallogr D Biol Crystallogr, 57, 1344-1347.
PDB codes: 1h4g 1h4h
11406577 J.M.van den Elsen, D.A.Kuntz, and D.R.Rose (2001).
Structure of Golgi alpha-mannosidase II: a target for inhibition of growth and metastasis of cancer cells.
  EMBO J, 20, 3008-3017.
PDB codes: 1hty 1hww 1hxk
11709165 M.Hrmova, J.N.Varghese, R.De Gori, B.J.Smith, H.Driguez, and G.B.Fincher (2001).
Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase.
  Structure, 9, 1005-1016.
PDB codes: 1ieq 1iev 1iew 1iex
11327856 W.Huang, L.Boju, L.Tkalec, H.Su, H.O.Yang, N.S.Gunay, R.J.Linhardt, Y.S.Kim, A.Matte, and M.Cygler (2001).
Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis.
  Biochemistry, 40, 2359-2372.
PDB codes: 1hm2 1hm3 1hmu 1hmw
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
11006547 C.S.Rye, and S.G.Withers (2000).
Glycosidase mechanisms.
  Curr Opin Chem Biol, 4, 573-580.  
10813837 D.G.Pritchard, J.O.Trent, X.Li, P.Zhang, M.L.Egan, and J.R.Baker (2000).
Characterization of the active site of group B streptococcal hyaluronan lyase.
  Proteins, 40, 126-134.  
10933800 D.O.Hart, S.He, C.J.Chany, S.G.Withers, P.F.Sims, M.L.Sinnott, and H.Brumer (2000).
Identification of Asp-130 as the catalytic nucleophile in the main alpha-galactosidase from Phanerochaete chrysosporium, a family 27 glycosyl hydrolase.
  Biochemistry, 39, 9826-9836.  
  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.  
10801342 J.Yang, S.Schenkman, and B.A.Horenstein (2000).
Primary 13C and beta-secondary 2H KIEs for trans-sialidase. A snapshot of nucleophilic participation during catalysis.
  Biochemistry, 39, 5902-5910.  
10805771 S.S.Parikh, G.Walcher, G.D.Jones, G.Slupphaug, H.E.Krokan, G.M.Blackburn, and J.A.Tainer (2000).
Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects.
  Proc Natl Acad Sci U S A, 97, 5083-5088.
PDB codes: 1emh 1emj
11042447 U.M.Unligil, and J.M.Rini (2000).
Glycosyltransferase structure and mechanism.
  Curr Opin Struct Biol, 10, 510-517.  
11032794 U.M.Unligil, S.Zhou, S.Yuwaraj, M.Sarkar, H.Schachter, and J.M.Rini (2000).
X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily.
  EMBO J, 19, 5269-5280.
PDB codes: 1fo8 1fo9 1foa
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
10821697 Y.Hou, D.Vocadlo, S.Withers, and D.Mahuran (2000).
Role of beta Arg211 in the active site of human beta-hexosaminidase B.
  Biochemistry, 39, 6219-6227.  
10381409 E.Sabini, G.Sulzenbacher, M.Dauter, Z.Dauter, P.L.Jørgensen, M.Schülein, C.Dupont, G.J.Davies, and K.S.Wilson (1999).
Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase.
  Chem Biol, 6, 483-492.
PDB codes: 1h4g 1h4h 1qh6 1qh7
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.