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PDBsum entry 1h13

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protein links
Hydrolase PDB id
1h13
Jmol
Contents
Protein chain
404 a.a. *
Waters ×432
* Residue conservation analysis
PDB id:
1h13
Name: Hydrolase
Title: Structure of a cold-adapted family 8 xylanase
Structure: Endo-1,4-beta-xylanase. Chain: a. Engineered: yes
Source: Pseudoalteromonas haloplanktis. Organism_taxid: 228. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.3Å     R-factor:   0.120     R-free:   0.146
Authors: F.Van Petegem,T.Collins,M.A.Meuwis,G.Feller,C.Gerday, J.Van Beeumen
Key ref:
F.Van Petegem et al. (2003). The structure of a cold-adapted family 8 xylanase at 1.3 A resolution. Structural adaptations to cold and investgation of the active site. J Biol Chem, 278, 7531-7539. PubMed id: 12475991 DOI: 10.1074/jbc.M206862200
Date:
02-Jul-02     Release date:   13-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8RJN8  (Q8RJN8_PSEHA) -  Endo-1,4-beta-xylanase (Precursor)
Seq:
Struc:
426 a.a.
404 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 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     catalytic activity     5 terms  

 

 
DOI no: 10.1074/jbc.M206862200 J Biol Chem 278:7531-7539 (2003)
PubMed id: 12475991  
 
 
The structure of a cold-adapted family 8 xylanase at 1.3 A resolution. Structural adaptations to cold and investgation of the active site.
F.Van Petegem, T.Collins, M.A.Meuwis, C.Gerday, G.Feller, J.Van Beeumen.
 
  ABSTRACT  
 
Enzymes from psychrophilic organisms differ from their mesophilic counterparts in having a lower thermostability and a higher specific activity at low and moderate temperatures. The current consensus is that they have an increased flexibility, enhancing accommodation and transformation of the substrates at low energy costs. Here we describe the structure of the xylanase from the Antarctic bacterium Pseudoalteromonas haloplanktis at 1.3 A resolution. Xylanases are usually grouped into glycosyl hydrolase families 10 and 11, but this enzyme belongs to family 8. The fold differs from that of other known xylanases and can be described as an (alpha/alpha)(6) barrel. Various parameters that may explain the cold-adapted properties were examined and indicated that the protein has a reduced number of salt bridges and an increased exposure of hydrophobic residues. The crystal structures of a complex with xylobiose and of mutant D144N were obtained at 1.2 and 1.5 A resolution, respectively. Analysis of the various substrate binding sites shows that the +3 and -3 subsites are rearranged as compared to those of a family 8 homolog, while the xylobiose complex suggests the existence of a +4 subsite. A decreased acidity of the substrate binding cleft and an increased flexibility of aromatic residues lining the subsites may enhance the rate at which substrate is bound.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Binding of xylobiose to pXyl. A, omit map of a complex of the enzyme with xylobiose, showing the positioning of the reducing end xylose in the xylanase structure. The map is contoured at 2 (pink), 3 (blue), and 4 (green). The refined coordinates for the xylosyl residue and for Tyr-378 are shown. B, LIGPLOT diagram showing the interactions between the xylosyl residue and protein residues/water molecules (dark gray spheres). Hydrogen bonds are represented by dashed lines. The side chain of Tyr-378 is in hydrophobic contact with the C-5 atom of the xylosyl residue.
Figure 6.
Fig. 6. Schematic representation of the geometry of the catalytic center of the wild type cold-adapted xylanase (A), the psychrophilic xylanase mutant D144N (B), and the native C. thermocellum endoglucanase CelA (C). Dashed lines indicate hydrogen bonds. Distances between residues not implicated in hydrogen bonding are shown by a double arrow. Hypothetical charges are shown as + or . All distances shown are in Å. For clarity, water atoms implicated in hydrogen bonds are not included.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 7531-7539) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21331632 S.Elleuche, H.Piascheck, and G.Antranikian (2011).
Fusion of the OsmC domain from esterase EstO confers thermolability to the cold-active xylanase Xyn8 from Pseudoalteromonas arctica.
  Extremophiles, 15, 311-317.  
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.  
20552357 A.Pollet, J.Schoepe, E.Dornez, S.V.Strelkov, J.A.Delcour, and C.M.Courtin (2010).
Functional analysis of glycoside hydrolase family 8 xylanases shows narrow but distinct substrate specificities and biotechnological potential.
  Appl Microbiol Biotechnol, 87, 2125-2135.  
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
19517107 D.Isogawa, T.Fukuda, K.Kuroda, H.Kusaoke, H.Kimoto, S.Suye, and M.Ueda (2009).
Demonstration of catalytic proton acceptor of chitosanase from Paenibacillus fukuinensis by comprehensive analysis of mutant library.
  Appl Microbiol Biotechnol, 85, 95.  
  19193992 H.L.Pedersen, N.P.Willassen, and I.Leiros (2009).
The first structure of a cold-adapted superoxide dismutase (SOD): biochemical and structural characterization of iron SOD from Aliivibrio salmonicida.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 84-92.
PDB code: 2w7w
18312599 C.Michaux, J.Massant, F.Kerff, J.M.Frère, J.D.Docquier, I.Vandenberghe, B.Samyn, A.Pierrard, G.Feller, P.Charlier, J.Van Beeumen, and J.Wouters (2008).
Crystal structure of a cold-adapted class C beta-lactamase.
  FEBS J, 275, 1687-1697.
PDB code: 2qz6
18368288 E.Stefanidi, and C.E.Vorgias (2008).
Molecular analysis of the gene encoding a new chitinase from the marine psychrophilic bacterium Moritella marina and biochemical characterization of the recombinant enzyme.
  Extremophiles, 12, 541-552.  
18320143 J.G.Berrin, and N.Juge (2008).
Factors affecting xylanase functionality in the degradation of arabinoxylans.
  Biotechnol Lett, 30, 1139-1150.  
17573938 T.L.Skovhus, C.Holmström, S.Kjelleberg, and I.Dahllöf (2007).
Molecular investigation of the distribution, abundance and diversity of the genus Pseudoalteromonas in marine samples.
  FEMS Microbiol Ecol, 61, 348-361.  
17235516 V.Spiwok, P.Lipovová, T.Skálová, J.Dusková, J.Dohnálek, J.Hasek, N.J.Russell, and B.Králová (2007).
Cold-active enzymes studied by comparative molecular dynamics simulation.
  J Mol Model, 13, 485-497.  
16532363 C.C.Lee, R.E.Kibblewhite-Accinelli, K.Wagschal, G.H.Robertson, and D.W.Wong (2006).
Cloning and characterization of a cold-active xylanase enzyme from an environmental DNA library.
  Extremophiles, 10, 295-300.  
16756497 K.S.Siddiqui, and R.Cavicchioli (2006).
Cold-adapted enzymes.
  Annu Rev Biochem, 75, 403-433.  
16804941 Y.Yasutake, S.Kawano, K.Tajima, M.Yao, Y.Satoh, M.Munekata, and I.Tanaka (2006).
Structural characterization of the Acetobacter xylinum endo-beta-1,4-glucanase CMCax required for cellulose biosynthesis.
  Proteins, 64, 1069-1077.
PDB code: 1wzz
  16511027 D.Dong, T.Ihara, H.Motoshima, and K.Watanabe (2005).
Crystallization and preliminary X-ray crystallographic studies of a psychrophilic subtilisin-like protease Apa1 from Antarctic Pseudoalteromonas sp. strain AS-11.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 308-311.  
15670163 J.Arnórsdóttir, M.M.Kristjánsson, and R.Ficner (2005).
Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation.
  FEBS J, 272, 832-845.
PDB codes: 1s2n 1sh7
  16511009 S.Kawano, Y.Yasutake, K.Tajima, Y.Satoh, M.Yao, I.Tanaka, and M.Munekata (2005).
Crystallization and preliminary crystallographic analysis of the cellulose biosynthesis-related protein CMCax from Acetobacter xylinum.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 252-254.  
15652973 T.Collins, C.Gerday, and G.Feller (2005).
Xylanases, xylanase families and extremophilic xylanases.
  FEMS Microbiol Rev, 29, 3.  
  16511021 Y.Honda, S.Fushinobu, M.Hidaka, T.Wakagi, H.Shoun, and M.Kitaoka (2005).
Crystallization and preliminary X-ray analysis of reducing-end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 291-292.  
  16233714 A.Hoyoux, V.Blaise, T.Collins, S.D'Amico, E.Gratia, A.L.Huston, J.C.Marx, G.Sonan, Y.Zeng, G.Feller, and C.Gerday (2004).
Extreme catalysts from low-temperature environments.
  J Biosci Bioeng, 98, 317-330.  
14975528 D.Georlette, V.Blaise, T.Collins, S.D'Amico, E.Gratia, A.Hoyoux, J.C.Marx, G.Sonan, G.Feller, and C.Gerday (2004).
Some like it cold: biocatalysis at low temperatures.
  FEMS Microbiol Rev, 28, 25-42.  
14993687 T.Parkkinen, N.Hakulinen, M.Tenkanen, M.Siika-aho, and J.Rouvinen (2004).
Crystallization and preliminary X-ray analysis of a novel Trichoderma reesei xylanase IV belonging to glycoside hydrolase family 5.
  Acta Crystallogr D Biol Crystallogr, 60, 542-544.  
12831897 D.Shallom, and Y.Shoham (2003).
Microbial hemicellulases.
  Curr Opin Microbiol, 6, 219-228.  
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.