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PDBsum entry 1t6g

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protein ligands Protein-protein interface(s) links
Hydrolase inhibitor PDB id
1t6g
Jmol
Contents
Protein chains
368 a.a. *
182 a.a. *
Ligands
GOL ×4
Waters ×1074
* Residue conservation analysis
PDB id:
1t6g
Name: Hydrolase inhibitor
Title: Crystal structure of the triticum aestivum xylanase inhibito complex with aspergillus niger xylanase-i
Structure: Xylanase inhibitor. Chain: a, b. Endo-1,4-beta-xylanase i. Chain: c, d. Synonym: xylanase i, 1,4-beta-d-xylan xylanohydrolase i. Ec: 3.2.1.8
Source: Triticum aestivum. Bread wheat. Organism_taxid: 4565. Other_details: purified from wheat flour. Aspergillus niger. Organism_taxid: 5061
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.162     R-free:   0.192
Authors: S.Sansen,C.J.De Ranter,K.Gebruers,K.Brijs,C.M.Courtin,J.A.De A.Rabijns
Key ref:
S.Sansen et al. (2004). Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I. J Biol Chem, 279, 36022-36028. PubMed id: 15166216 DOI: 10.1074/jbc.M404212200
Date:
06-May-04     Release date:   28-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8H0K8  (Q8H0K8_WHEAT) -  Xylanase inhibitor
Seq:
Struc:
402 a.a.
368 a.a.
Protein chains
Pfam   ArchSchema ?
P55329  (XYNA_ASPNG) -  Endo-1,4-beta-xylanase A
Seq:
Struc:
211 a.a.
182 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains C, D: 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   5 terms 
  Biochemical function     hydrolase activity     5 terms  

 

 
DOI no: 10.1074/jbc.M404212200 J Biol Chem 279:36022-36028 (2004)
PubMed id: 15166216  
 
 
Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I.
S.Sansen, C.J.De Ranter, K.Gebruers, K.Brijs, C.M.Courtin, J.A.Delcour, A.Rabijns.
 
  ABSTRACT  
 
Plants developed a diverse battery of defense mechanisms in response to continual challenges by a broad spectrum of pathogenic microorganisms. Their defense arsenal includes inhibitors of cell wall-degrading enzymes, which hinder a possible invasion and colonization by antagonists. The structure of Triticum aestivum xylanase inhibitor-I (TAXI-I), a first member of potent TAXI-type inhibitors of fungal and bacterial family 11 xylanases, has been determined to 1.7-A resolution. Surprisingly, TAXI-I displays structural homology with the pepsin-like family of aspartic proteases but is proteolytically nonfunctional, because one or more residues of the essential catalytical triad are absent. The structure of the TAXI-I.Aspergillus niger xylanase I complex, at a resolution of 1.8 A, illustrates the ability of tight binding and inhibition with subnanomolar affinity and indicates the importance of the C-terminal end for the differences in xylanase specificity among different TAXI-type inhibitors.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Overall structure of TAXI-I. A, ribbon diagram of TAXI-I, generated using MolScript (45). The secondary structure elements are marked. B, folding topology diagram of TAXI-I, nomenclature and colors are in accordance with A. -strands are shown as arrows, -helices as long rectangles, 3[10]-helical fragments as small boxes. These 3[10]-fragments were omitted in A for clarity. The composition of the -sheets B, N1, N2, N3, C1, C2, and C3 is indicated. In both A and B, the position of the cleavage site is marked. TAXI-I form B is believed to result from a proteolytical cleavage of TAXI-I form A after Asn265 (16).
Figure 3.
FIG. 3. A, overall structure of the ANXI·TAXI-I complex. Ribbon diagram of TAXI-I (orange) in complex with ANXI (light blue, thumb region in cyan). Five TAXI-I loop regions (L[NiNj], L[HdCk], L[HfCs], L[HhCy], and L[CzCterm]) completely cover the deep substrate-binding and active site cleft of the xylanase and are displayed in violet. His374 on the C-terminal loop L[CzCterm] is shown in sticks and is located in between the two active site glutamic acids of the xylanase (sticks). The substrate-binding groove of the pepsin-like aspartic proteases (arrowed) is clearly distinct from the TAXI-I-ANXI interaction region. The knottin-like motif is boxed. B, a detailed view on the key interactions of the inhibition. The imidazole ring of His374 on loop L[CzCterm] of TAXI-I (orange) is located in between the two catalytic residues (Glu79 and Glu170) of ANXI and is strongly hydrogen bonded to Asp37. In a superimposition of the structure of a catalytically inactive B. circulans xylanase mutant complexed with xylobiose (PDB code 1bcx [PDB] ) (36) (in subsite -1 and -2) with the structure of the ANXI·TAXI-I complex, Leu292 on loop L[HfCs] perfectly mimics the position of a xylose molecule in subsite -2.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 36022-36028) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21457461 T.Yoshizawa, T.Shimizu, M.Yamabe, M.Taichi, Y.Nishiuchi, N.Shichijo, S.Unzai, H.Hirano, M.Sato, and H.Hashimoto (2011).
Crystal structure of basic 7S globulin, a xyloglucan-specific endo-β-1,4-glucanase inhibitor protein-like protein from soybean lacking inhibitory activity against endo-β-glucanase.
  FEBS J, 278, 1944-1954.
PDB code: 3aup
20699573 A.D.Shutov, K.Prak, T.Fukuda, S.V.Rudakov, A.S.Rudakova, M.R.Tandang-Silvas, K.Fujiwara, B.Mikami, S.Utsumi, and N.Maruyama (2010).
Soybean basic 7S globulin: subunit heterogeneity and molecular evolution.
  Biosci Biotechnol Biochem, 74, 1631-1634.  
20544973 E.Vandermarliere, W.Lammens, J.Schoepe, S.Rombouts, E.Fierens, K.Gebruers, G.Volckaert, A.Rabijns, J.A.Delcour, S.V.Strelkov, and C.M.Courtin (2010).
Crystal structure of the noncompetitive xylanase inhibitor TLXI, member of the small thaumatin-like protein family.
  Proteins, 78, 2391-2394.
PDB code: 3g7m
20066263 T.M.Gloster, and G.J.Davies (2010).
Glycosidase inhibition: assessing mimicry of the transition state.
  Org Biomol Chem, 8, 305-320.  
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
19769747 A.Pollet, S.Sansen, G.Raedschelders, K.Gebruers, A.Rabijns, J.A.Delcour, and C.M.Courtin (2009).
Identification of structural determinants for inhibition strength and specificity of wheat xylanase inhibitors TAXI-IA and TAXI-IIA.
  FEBS J, 276, 3916-3927.
PDB codes: 2b42 3hd8
19758436 N.D.Rawlings, and A.Bateman (2009).
Pepsin homologues in bacteria.
  BMC Genomics, 10, 437.  
19452551 N.Kowalsman, and M.Eisenstein (2009).
Combining interface core and whole interface descriptors in postscan processing of protein-protein docking models.
  Proteins, 77, 297-318.  
19497379 S.Lagaert, T.Beliën, and G.Volckaert (2009).
Plant cell walls: Protecting the barrier from degradation by microbial enzymes.
  Semin Cell Dev Biol, 20, 1064-1073.  
17729269 A.May, and M.Zacharias (2008).
Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking.
  Proteins, 70, 794-809.  
18340629 E.Croes, K.Gebruers, J.Robben, J.P.Noben, B.Samyn, G.Debyser, J.Van Beeumen, J.A.Delcour, and C.M.Courtin (2008).
Variability of polymorphic families of three types of xylanase inhibitors in the wheat grain proteome.
  Proteomics, 8, 1692-1705.  
18210371 E.Jamet, C.Albenne, G.Boudart, M.Irshad, H.Canut, and R.Pont-Lezica (2008).
Recent advances in plant cell wall proteomics.
  Proteomics, 8, 893-908.  
18550418 J.C.Misas-Villamil, and R.A.van der Hoorn (2008).
Enzyme-inhibitor interactions at the plant-pathogen interface.
  Curr Opin Plant Biol, 11, 380-388.  
18320143 J.G.Berrin, and N.Juge (2008).
Factors affecting xylanase functionality in the degradation of arabinoxylans.
  Biotechnol Lett, 30, 1139-1150.  
17803233 N.London, and O.Schueler-Furman (2007).
Assessing the energy landscape of CAPRI targets by FunHunt.
  Proteins, 69, 809-815.  
17803234 S.J.de Vries, A.D.van Dijk, M.Krzeminski, M.van Dijk, A.Thureau, V.Hsu, T.Wassenaar, and A.M.Bonvin (2007).
HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets.
  Proteins, 69, 726-733.  
17393541 T.Beliën, S.Van Campenhout, A.Vanden Bosch, T.M.Bourgois, S.Rombouts, J.Robben, C.M.Courtin, J.A.Delcour, and G.Volckaert (2007).
Engineering molecular recognition of endoxylanase enzymes and their inhibitors through phage display.
  J Mol Recognit, 20, 103-112.  
17513587 T.Beliën, S.Van Campenhout, M.Van Acker, J.Robben, C.M.Courtin, J.A.Delcour, and G.Volckaert (2007).
Mutational analysis of endoxylanases XylA and XylB from the phytopathogen Fusarium graminearum reveals comprehensive insights into their inhibitor insensitivity.
  Appl Environ Microbiol, 73, 4602-4608.  
17444519 T.M.Cheng, T.L.Blundell, and J.Fernandez-Recio (2007).
pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking.
  Proteins, 68, 503-515.  
16506242 C.J.Camacho, H.Ma, and P.C.Champ (2006).
Scoring a diverse set of high-quality docked conformations: a metascore based on electrostatic and desolvation interactions.
  Proteins, 63, 868-877.  
16774842 N.Juge (2006).
Plant protein inhibitors of cell wall degrading enzymes.
  Trends Plant Sci, 11, 359-367.  
17022171 T.Beliën, S.Van Campenhout, J.Robben, and G.Volckaert (2006).
Microbial endoxylanases: effective weapons to breach the plant cell-wall barrier or, rather, triggers of plant defense systems?
  Mol Plant Microbe Interact, 19, 1072-1081.  
15981252 A.D.van Dijk, S.J.de Vries, C.Dominguez, H.Chen, H.X.Zhou, and A.M.Bonvin (2005).
Data-driven docking: HADDOCK's adventures in CAPRI.
  Proteins, 60, 232-238.  
15981253 C.J.Camacho (2005).
Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets.
  Proteins, 60, 245-251.  
15981255 C.Zhang, S.Liu, and Y.Zhou (2005).
Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function.
  Proteins, 60, 314-318.  
15981246 D.Law, M.Hotchko, and L.Ten Eyck (2005).
Progress in computation and amide hydrogen exchange for prediction of protein-protein complexes.
  Proteins, 60, 302-307.  
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.  
15981258 G.R.Smith, P.W.Fitzjohn, C.S.Page, and P.A.Bates (2005).
Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI.
  Proteins, 60, 263-268.  
15981245 G.Terashi, M.Takeda-Shitaka, D.Takaya, K.Komatsu, and H.Umeyama (2005).
Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues.
  Proteins, 60, 289-295.  
16080151 H.Chen, and H.X.Zhou (2005).
Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data.
  Proteins, 61, 21-35.  
15659362 J.Janin (2005).
Assessing predictions of protein-protein interaction: the CAPRI experiment.
  Protein Sci, 14, 278-283.  
15981267 J.Janin (2005).
The targets of CAPRI rounds 3-5.
  Proteins, 60, 170-175.  
16279951 K.Fierens, A.Gils, S.Sansen, K.Brijs, C.M.Courtin, P.J.Declerck, C.J.De Ranter, K.Gebruers, A.Rabijns, J.Robben, S.Campenhout, G.Volckaert, and J.A.Delcour (2005).
His374 of wheat endoxylanase inhibitor TAXI-I stabilizes complex formation with glycoside hydrolase family 11 endoxylanases.
  FEBS J, 272, 5872-5882.  
15981263 K.Wiehe, B.Pierce, J.Mintseris, W.W.Tong, R.Anderson, R.Chen, and Z.Weng (2005).
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5.
  Proteins, 60, 207-213.  
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.  
15981270 M.Zacharias (2005).
ATTRACT: protein-protein docking in CAPRI using a reduced protein model.
  Proteins, 60, 252-256.  
15981249 O.Schueler-Furman, C.Wang, and D.Baker (2005).
Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.
  Proteins, 60, 187-194.  
15981271 P.Carter, V.I.Lesk, S.A.Islam, and M.J.Sternberg (2005).
Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI.
  Proteins, 60, 281-288.  
15981265 S.R.Comeau, S.Vajda, and C.J.Camacho (2005).
Performance of the first protein docking server ClusPro in CAPRI rounds 3-5.
  Proteins, 60, 239-244.  
15914935 T.Igawa, T.Tokai, T.Kudo, I.Yamaguchi, and M.Kimura (2005).
A wheat xylanase inhibitor gene, Xip-I, but not Taxi-I, is significantly induced by biotic and abiotic signals that trigger plant defense.
  Biosci Biotechnol Biochem, 69, 1058-1063.  
15981251 Y.Inbar, D.Schneidman-Duhovny, I.Halperin, A.Oron, R.Nussinov, and H.J.Wolfson (2005).
Approaching the CAPRI challenge with an efficient geometry-based docking.
  Proteins, 60, 217-223.  
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.