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PDBsum entry 1bg4

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protein ligands metals links
Family 10 xylanase PDB id
1bg4
Jmol
Contents
Protein chain
302 a.a. *
Ligands
TRS ×2
GOL ×7
Metals
_NA ×6
Waters ×316
* Residue conservation analysis
PDB id:
1bg4
Name: Family 10 xylanase
Title: Xylanase from penicillium simplicissimum
Structure: Endo-1,4-beta-xylanase. Chain: a. Ec: 3.2.1.8
Source: Penicillium simplicissimum. Organism_taxid: 69488. Collection: bt 2246, culture collection of the institute of biotechnology, university of technology, graz, austria. Cellular_location: secreted. Other_details: penicillium simplicissimum (oudem.) Thom
Resolution:
1.75Å     R-factor:   0.200     R-free:   0.229
Authors: A.Schmidt,C.Kratky
Key ref: A.Schmidt et al. (1998). Structure of the xylanase from Penicillium simplicissimum. Protein Sci, 7, 2081-2088. PubMed id: 9792094 DOI: 10.1002/pro.5560071004
Date:
05-Jun-98     Release date:   12-Aug-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56588  (XYNA_PENSI) -  Endo-1,4-beta-xylanase
Seq:
Struc:
302 a.a.
302 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!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1002/pro.5560071004 Protein Sci 7:2081-2088 (1998)
PubMed id: 9792094  
 
 
Structure of the xylanase from Penicillium simplicissimum.
A.Schmidt, A.Schlacher, W.Steiner, H.Schwab, C.Kratky.
 
  ABSTRACT  
 
Despite its relatively low pH and temperature optimum, the xylanase from Penicillium simplicissimum performs exceedingly well under conditions of paper bleaching. We have purified and characterized this enzyme, which belongs to family 10 of glycosyl hydrolases. Its gene was cloned, and the sequence of the protein was deduced from the nucleotide sequence. The xylanase was crystallized from ammonium sulfate at pH 8.4, and X-ray data were collected at cryo-temperature to a crystallographic resolution of 1.75 A. The crystal structure was solved by molecular replacement using the catalytic domain of the Clostridium thermocellum xylanase as a search model, and refined to a residual of R = 20% (R(free) = 23%) for data between 10 and 1.75 A. The xylanase folds in an (alpha/beta)8 barrel (TIM-barrel), with additional helices and loops arranged at the "top" forming the active site cleft. In its overall shape, the P. simplicissimum xylanase structure is similar to other family 10 xylanases, but its active site cleft is much shallower and wider. This probably accounts for the differences in catalysis and in the mode of action of this enzyme. Three glycerol molecules were observed to bind within the active site groove, one of which interacts directly with the catalytic glutamate residues. It appears that they occupy putative xylose binding subsites.
 

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.  
18320143 J.G.Berrin, and N.Juge (2008).
Factors affecting xylanase functionality in the degradation of arabinoxylans.
  Biotechnol Lett, 30, 1139-1150.  
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.  
17642511 V.Solomon, A.Teplitsky, S.Shulami, G.Zolotnitsky, Y.Shoham, and G.Shoham (2007).
Structure-specificity relationships of an intracellular xylanase from Geobacillus stearothermophilus.
  Acta Crystallogr D Biol Crystallogr, 63, 845-859.
PDB code: 2q8x
15988573 H.Tanaka, M.Muguruma, and K.Ohta (2006).
Purification and properties of a family-10 xylanase from Aureobasidium pullulans ATCC 20524 and characterization of the encoding gene.
  Appl Microbiol Biotechnol, 70, 202-211.  
16823036 K.Manikandan, A.Bhardwaj, N.Gupta, N.K.Lokanath, A.Ghosh, V.S.Reddy, and S.Ramakumar (2006).
Crystal structures of native and xylosaccharide-bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG-27: structural insights into alkalophilicity and implications for adaptation to polyextreme conditions.
  Protein Sci, 15, 1951-1960.
PDB codes: 2f8q 2fgl
16972282 Z.Zhou, M.Bates, and J.D.Madura (2006).
Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design.
  Proteins, 65, 580-592.  
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.  
16247799 Ihsanawati, T.Kumasaka, T.Kaneko, C.Morokuma, R.Yatsunami, T.Sato, S.Nakamura, and N.Tanaka (2005).
Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.
  Proteins, 61, 999.
PDB codes: 1vbr 1vbu
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.  
15652973 T.Collins, C.Gerday, and G.Feller (2005).
Xylanases, xylanase families and extremophilic xylanases.
  FEMS Microbiol Rev, 29, 3.  
  16511010 Z.Fujimoto, K.Usui, Y.Kondo, K.Yasui, K.Kawai, and T.Suzuki (2005).
Crystallization and preliminary X-ray crystallographic studies of XynX, a family 10 xylanase from Aeromonas punctata ME-1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 255-257.  
15103129 A.Teplitsky, A.Mechaly, V.Stojanoff, G.Sainz, G.Golan, H.Feinberg, R.Gilboa, V.Reiland, G.Zolotnitsky, D.Shallom, A.Thompson, Y.Shoham, and G.Shoham (2004).
Structure determination of the extracellular xylanase from Geobacillus stearothermophilus by selenomethionyl MAD phasing.
  Acta Crystallogr D Biol Crystallogr, 60, 836-848.
PDB code: 1hiz
15277671 G.Zolotnitsky, U.Cogan, N.Adir, V.Solomon, G.Shoham, and Y.Shoham (2004).
Mapping glycoside hydrolase substrate subsites by isothermal titration calorimetry.
  Proc Natl Acad Sci U S A, 101, 11275-11280.
PDB codes: 1r85 1r87
12876348 A.Canals, M.C.Vega, F.X.Gomis-Rüth, M.Díaz, R.I.Santamaría R, and M.Coll (2003).
Structure of xylanase Xys1delta from Streptomyces halstedii.
  Acta Crystallogr D Biol Crystallogr, 59, 1447-1453.
PDB code: 1nq6
12925805 Ihsanawati, T.Kumasaka, T.Kaneko, C.Morokuma, S.Nakamura, and N.Tanaka (2003).
Crystallization and preliminary X-ray studies of xylanase 10B from Thermotoga maritima.
  Acta Crystallogr D Biol Crystallogr, 59, 1659-1661.  
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
11358504 S.P.George, and M.B.Rao (2001).
Conformation and polarity of the active site of xylanase I from Thermomonospora sp. as deduced by fluorescent chemoaffinity labeling. Site and significance of a histidine residue.
  Eur J Biochem, 268, 2881-2888.  
11223515 S.Teixeira, L.Lo Leggio, R.Pickersgill, and C.Cardin (2001).
Anisotropic refinement of the structure of Thermoascus aurantiacus xylanase I.
  Acta Crystallogr D Biol Crystallogr, 57, 385-392.
PDB code: 1fxm
10675327 F.Vallée, F.Lipari, P.Yip, B.Sleno, A.Herscovics, and P.L.Howell (2000).
Crystal structure of a class I alpha1,2-mannosidase involved in N-glycan processing and endoplasmic reticulum quality control.
  EMBO J, 19, 581-588.
PDB code: 1dl2
11055928 I.Zadra, B.Abt, W.Parson, and H.Haas (2000).
xylP promoter-based expression system and its use for antisense downregulation of the Penicillium chrysogenum nitrogen regulator NRE.
  Appl Environ Microbiol, 66, 4810-4816.  
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
11123890 M.D.Hulett, J.R.Hornby, S.J.Ohms, J.Zuegg, C.Freeman, J.E.Gready, and C.R.Parish (2000).
Identification of active-site residues of the pro-metastatic endoglycosidase heparanase.
  Biochemistry, 39, 15659-15667.  
  10548044 J.Zuegg, K.Gruber, M.Gugganig, U.G.Wagner, and C.Kratky (1999).
Three-dimensional structures of enzyme-substrate complexes of the hydroxynitrile lyase from Hevea brasiliensis.
  Protein Sci, 8, 1990-2000.
PDB codes: 2yas 3yas 4yas 5yas 6yas 7yas
10570988 Y.Sato, Y.Niimura, K.Yura, and M.Go (1999).
Module-intron correlation and intron sliding in family F/10 xylanase genes.
  Gene, 238, 93.  
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.