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PDBsum entry 1qh6

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Hydrolase PDB id
1qh6
Jmol
Contents
Protein chains
207 a.a. *
Ligands
FXP ×2
Waters ×539
* Residue conservation analysis
PDB id:
1qh6
Name: Hydrolase
Title: Catalysis and specificity in enzymatic glycoside hydrolases: a 2,5b conformation for the glycosyl-enzyme intermidiate revealed by the structure of the bacillus agaradhaerens family 11 xylanase
Structure: Xylanase. Chain: a, b. Fragment: family 11 xylanase catalytic domain. Engineered: yes. Other_details: b-d-xylanopyranoside present in the active site
Source: Bacillus agaradhaerens. Organism_taxid: 76935. Expressed in: bacillus subtilis. Expression_system_taxid: 1423
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.142     R-free:   0.189
Authors: E.Sabini,G.Sulzenbacher,M.Dauter,Z.Dauter,P.L.Jorgensen, M.Schulein,C.Dupont,G.J.Davies,K.S.Wilson
Key ref: E.Sabini et al. (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. PubMed id: 10381409
Date:
11-May-99     Release date:   17-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q7SIE3  (Q7SIE3_BACAG) -  Endo-1,4-beta-xylanase
Seq:
Struc:
207 a.a.
207 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   3 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
Chem Biol 6:483-492 (1999)
PubMed id: 10381409  
 
 
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.
E.Sabini, G.Sulzenbacher, M.Dauter, Z.Dauter, P.L.Jørgensen, M.Schülein, C.Dupont, G.J.Davies, K.S.Wilson.
 
  ABSTRACT  
 
BACKGROUND: The enzymatic hydrolysis of glycosides involves the formation and subsequent breakdown of a covalent glycosyl-enzyme intermediate via oxocarbenium-ion-like transition states. The covalent intermediate may be trapped on-enzyme using 2-fluoro-substituted glycosides, which provide details of the intermediate conformation and noncovalent interactions between enzyme and oligosaccharide. Xylanases are important in industrial applications - in the pulp and paper industry, pretreating wood with xylanases decreases the amount of chlorine-containing chemicals used. Xylanases are structurally similar to cellulases but differ in their specificity for xylose-based, versus glucose-based, substrates. RESULTS: The structure of the family 11 xylanase, Xyl11, from Bacillus agaradhaerens has been solved using X-ray crystallography in both native and xylobiosyl-enzyme intermediate forms at 1.78 A and 2.0 A resolution, respectively. The covalent glycosyl-enzyme intermediate has been trapped using a 2-fluoro-2-deoxy substrate with a good leaving group. Unlike covalent intermediate structures for glycoside hydrolases from other families, the covalent glycosyl-enzyme intermediate in family 11 adopts an unusual 2,5B conformation. CONCLUSIONS: The 2,5B conformation found for the alpha-linked xylobiosyl-enzyme intermediate of Xyl11, unlike the 4C1 chair conformation observed for other systems, is consistent with the stereochemical constraints required of the oxocarbenium-ion-like transition state. Comparison of the Xyl11 covalent glycosyl-enzyme intermediate with the equivalent structure for the related family 12 endoglucanase, CelB, from Streptomyces lividans reveals the likely determinants for substrate specificity in this clan of glycoside hydrolases.
 

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.  
20868223 D.R.Carrillo, C.Parthier, N.Jänckel, J.Grandke, M.Stelter, S.Schilling, M.Boehme, P.Neumann, R.Wolf, H.U.Demuth, M.T.Stubbs, and J.U.Rahfeld (2010).
Kinetic and structural characterization of bacterial glutaminyl cyclases from Zymomonas mobilis and Myxococcus xanthus.
  Biol Chem, 391, 1419-1428.
PDB codes: 3nok 3nol 3nom
18853398 J.M.Schmidt, M.J.Howard, M.Maestre-Martínez, C.S.Pérez, and F.Löhr (2009).
Variation in protein C(alpha)-related one-bond J couplings.
  Magn Reson Chem, 47, 16-30.  
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.  
19269961 R.Carapito, A.Imberty, J.M.Jeltsch, S.C.Byrns, P.H.Tam, T.L.Lowary, A.Varrot, and V.Phalip (2009).
Molecular Basis of Arabinobio-hydrolase Activity in Phytopathogenic Fungi: CRYSTAL STRUCTURE AND CATALYTIC MECHANISM OF FUSARIUM GRAMINEARUM GH93 EXO-{alpha}-L-ARABINANASE.
  J Biol Chem, 284, 12285-12296.
PDB codes: 2w5n 2w5o
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.  
17237975 F.Löhr, R.Hänsel, V.V.Rogov, and V.Dötsch (2007).
Improved pulse sequences for sequence specific assignment of aromatic proton resonances in proteins.
  J Biomol NMR, 37, 205-224.  
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
16823793 V.A.Money, N.L.Smith, A.Scaffidi, R.V.Stick, H.J.Gilbert, and G.J.Davies (2006).
Substrate distortion by a lichenase highlights the different conformational itineraries harnessed by related glycoside hydrolases.
  Angew Chem Int Ed Engl, 45, 5136-5140.
PDB codes: 2cip 2cit
15987675 E.J.Taylor, A.Goyal, C.I.Guerreiro, J.A.Prates, V.A.Money, N.Ferry, C.Morland, A.Planas, J.A.Macdonald, R.V.Stick, H.J.Gilbert, C.M.Fontes, and G.J.Davies (2005).
How family 26 glycoside hydrolases orchestrate catalysis on different polysaccharides: structure and activity of a Clostridium thermocellum lichenase, CtLic26A.
  J Biol Chem, 280, 32761-32767.
PDB codes: 2bv9 2bvd
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.  
16211484 F.Löhr, V.V.Rogov, M.Shi, F.Bernhard, and V.Dötsch (2005).
Triple-resonance methods for complete resonance assignment of aromatic protons and directly bound heteronuclei in histidine and tryptophan residues.
  J Biomol NMR, 32, 309-328.  
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.  
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
  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.  
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
15159558 H.Novoa De Armas, C.Verboven, C.De Ranter, J.Desair, A.Vande Broek, J.Vanderleyden, and A.Rabijns (2004).
Azospirillum irakense pectate lyase displays a toroidal fold.
  Acta Crystallogr D Biol Crystallogr, 60, 999.
PDB code: 1r76
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.  
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
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.  
11937059 D.Nurizzo, T.Nagy, H.J.Gilbert, and G.J.Davies (2002).
The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A.
  Structure, 10, 547-556.
PDB codes: 1gqi 1gqj 1gqk 1gql
12221284 S.J.Charnock, I.E.Brown, J.P.Turkenburg, G.W.Black, and G.J.Davies (2002).
Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases.
  Proc Natl Acad Sci U S A, 99, 12067-12072.
PDB codes: 1gxm 1gxn 1gxo
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.  
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
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
11353474 S.K.Das, J.M.Mallet, J.Esnault, P.A.Driguez, P.Duchaussoy, P.Sizun, J.P.Hérault, J.M.Herbert, M.Petitou, and P.Sinaÿ (2001).
Synthesis of Conformationally Locked Carbohydrates: A Skew-Boat Conformation of L-Iduronic Acid Governs the Antithrombotic Activity of Heparin.
  Angew Chem Int Ed Engl, 40, 1670-1673.  
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.  
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
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.