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PDBsum entry 1us2

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protein ligands links
Hydrolase PDB id
1us2
Jmol
Contents
Protein chain
507 a.a. *
Ligands
XYP-XYP-XYP-XYP ×2
Waters ×833
* Residue conservation analysis
PDB id:
1us2
Name: Hydrolase
Title: Xylanase10c (mutant e385a) from cellvibrio japonicus in complex with xylopentaose
Structure: Endo-beta-1,4-xylanase. Chain: a. Fragment: carbohydrate binding module and catalytic module, residues (86-606). Synonym: xylanase10c. Engineered: yes. Mutation: yes
Source: Cellvibrio japonicus. Organism_taxid: 155077. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.85Å     R-factor:   0.181     R-free:   0.226
Authors: G.Pell,L.Szabo,S.J.Charnock,H.Xie,T.M.Gloster,G.J.Davies, H.
Key ref:
G.Pell et al. (2004). Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases. J Biol Chem, 279, 11777-11788. PubMed id: 14670951 DOI: 10.1074/jbc.M311947200
Date:
17-Nov-03     Release date:   18-Dec-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q59675  (Q59675_9GAMM) -  Endo-beta-1,4-xylanase Xyn10C
Seq:
Struc:
 
Seq:
Struc:
606 a.a.
507 a.a.*
Key:    PfamA domain  PfamB 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     carbohydrate metabolic process   1 term 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     1 term  

 

 
DOI no: 10.1074/jbc.M311947200 J Biol Chem 279:11777-11788 (2004)
PubMed id: 14670951  
 
 
Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases.
G.Pell, L.Szabo, S.J.Charnock, H.Xie, T.M.Gloster, G.J.Davies, H.J.Gilbert.
 
  ABSTRACT  
 
Microbial degradation of the plant cell wall is the primary mechanism by which carbon is utilized in the biosphere. The hydrolysis of xylan, by endo-beta-1,4-xylanases (xylanases), is one of the key reactions in this process. Although amino acid sequence variations are evident in the substrate binding cleft of "family GH10" xylanases (see afmb.cnrs-mrs.fr/CAZY/), their biochemical significance is unclear. The Cellvibrio japonicus GH10 xylanase CjXyn10C is a bi-modular enzyme comprising a GH10 catalytic module and a family 15 carbohydrate-binding module. The three-dimensional structure at 1.85 A, presented here, shows that the sequence joining the two modules is disordered, confirming that linker sequences in modular glycoside hydrolases are highly flexible. CjXyn10C hydrolyzes xylan at a rate similar to other previously described GH10 enzymes but displays very low activity against xylooligosaccharides. The poor activity on short substrates reflects weak binding at the -2 subsite of the enzyme. Comparison of CjXyn10C with other family GH10 enzymes reveals "polymorphisms" in the substrate binding cleft including a glutamate/glycine substitution at the -2 subsite and a tyrosine insertion in the -2/-3 glycone region of the substrate binding cleft, both of which contribute to the unusual properties of the enzyme. The CjXyn10C-substrate complex shows that Tyr-340 stacks against the xylose residue located at the -3 subsite, and the properties of Y340A support the view that this tyrosine plays a pivotal role in substrate binding at this location. The generic importance of using CjXyn10C as a template in predicting the biochemical properties of GH10 xylanases is discussed.
 
  Selected figure(s)  
 
Figure 5.
FIG. 5. Schematic representation of the protein-ligand interactions in the -4 to -1 subsites of CjXyn10C. Only direct hydrogen-bonding residues (with H-bond distances of <3.2 Å) and important aromatic/hydrophobic side chains mentioned in the text are shown.
Figure 7.
FIG. 7. Schematic of xylan hydrolysis by the xylan degrading enzymes of C. japonicus. The structures shown for CjXyn11A and CjXyn11B are representative bacterial GH11 enzymes from Bacillus agaradhaerens and Nonomuraea flexuosa, respectively, the structure shown for CjAbf51A is from Geobacillus stearothermophilus, and the structure shown for CjXyn10D is of the homologous (93% similar) enzyme CmXyn10B from C. mixtus. The enzymes CjAbf51A, CjGlcA67A, and CjXyn10C are all attached to the outer membrane of the bacterium, whereas CjXyn10A, CjXyn11A, and CjXyn11B are secreted into the culture medium (40, 42, 43). The sugar side chains released by the -glucuronidase and arabinofuranosidase, respectively, are likely to be transported into the cytoplasm of C. japonicus. (The depiction of the plant cell wall is reproduced from Carpita and Gieaut (44). Reproduced with permission from Blackwell Publishing, ©1993.)
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 11777-11788) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21393568 J.L.Brás, A.Cartmell, A.L.Carvalho, G.Verzé, E.A.Bayer, Y.Vazana, M.A.Correia, J.A.Prates, S.Ratnaparkhe, A.B.Boraston, M.J.Romão, C.M.Fontes, and H.J.Gilbert (2011).
Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis.
  Proc Natl Acad Sci U S A, 108, 5237-5242.
PDB code: 2xqo
21466666 M.Lafond, A.Tauzin, V.Desseaux, E.Bonnin, e.l.-.H.Ajandouz, and T.Giardina (2011).
GH10 xylanase D from Penicillium funiculosum: biochemical studies and xylooligosaccharide production.
  Microb Cell Fact, 10, 20.  
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.  
20696902 C.Hervé, A.Rogowski, A.W.Blake, S.E.Marcus, H.J.Gilbert, and J.P.Knox (2010).
Carbohydrate-binding modules promote the enzymatic deconstruction of intact plant cell walls by targeting and proximity effects.
  Proc Natl Acad Sci U S A, 107, 15293-15298.  
20589642 S.Qin, and H.X.Zhou (2010).
Selection of near-native poses in CAPRI rounds 13-19.
  Proteins, 78, 3166-3173.  
  20431716 D.Dodd, and I.K.Cann (2009).
Enzymatic deconstruction of xylan for biofuel production.
  Glob Change Biol Bioenergy, 1, 2.  
18688581 J.Y.Sun, M.Q.Liu, and X.Y.Weng (2009).
Hydrolytic properties of a hybrid xylanase and its parents.
  Appl Biochem Biotechnol, 152, 428-439.  
18799462 A.Cartmell, E.Topakas, V.M.Ducros, M.D.Suits, G.J.Davies, and H.J.Gilbert (2008).
The Cellvibrio japonicus mannanase CjMan26C displays a unique exo-mode of action that is conferred by subtle changes to the distal region of the active site.
  J Biol Chem, 283, 34403-34413.
PDB codes: 2vx4 2vx5 2vx6 2vx7
18320143 J.G.Berrin, and N.Juge (2008).
Factors affecting xylanase functionality in the degradation of arabinoxylans.
  Biotechnol Lett, 30, 1139-1150.  
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
17028274 F.J.St John, J.D.Rice, and J.F.Preston (2006).
Characterization of XynC from Bacillus subtilis subsp. subtilis strain 168 and analysis of its role in depolymerization of glucuronoxylan.
  J Bacteriol, 188, 8617-8626.  
16461704 F.J.Stjohn, J.D.Rice, and J.F.Preston (2006).
Paenibacillus sp. strain JDR-2 and XynA1: a novel system for methylglucuronoxylan utilization.
  Appl Environ Microbiol, 72, 1496-1506.  
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.  
16522374 K.A.Gray, L.Zhao, and M.Emptage (2006).
Bioethanol.
  Curr Opin Chem Biol, 10, 141-146.  
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
16717424 M.Sugimura, M.Nishimoto, and M.Kitaoka (2006).
Characterization of glycosynthase mutants derived from glycoside hydrolase family 10 xylanases.
  Biosci Biotechnol Biochem, 70, 1210-1217.  
15653742 I.von Ossowski, J.T.Eaton, M.Czjzek, S.J.Perkins, T.P.Frandsen, M.Schülein, P.Panine, B.Henrissat, and V.Receveur-Bréchot (2005).
Protein disorder: conformational distribution of the flexible linker in a chimeric double cellulase.
  Biophys J, 88, 2823-2832.  
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
  16511146 K.Manikandan, A.Bhardwaj, A.Ghosh, V.S.Reddy, and S.Ramakumar (2005).
Crystallization and preliminary X-ray study of a family 10 alkali-thermostable xylanase from alkalophilic Bacillus sp. strain NG-27.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 747-749.  
15914908 M.Nishimoto, M.Kitaoka, S.Fushinobu, and K.Hayashi (2005).
The role of conserved arginine residue in loop 4 of glycoside hydrolase family 10 xylanases.
  Biosci Biotechnol Biochem, 69, 904-910.  
15708971 M.R.Proctor, E.J.Taylor, D.Nurizzo, J.P.Turkenburg, R.M.Lloyd, M.Vardakou, G.J.Davies, and H.J.Gilbert (2005).
Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A.
  Proc Natl Acad Sci U S A, 102, 2697-2702.
PDB code: 1uv4
15652973 T.Collins, C.Gerday, and G.Feller (2005).
Xylanases, xylanase families and extremophilic xylanases.
  FEMS Microbiol Rev, 29, 3.  
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
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.