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PDBsum entry 1ta3

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protein ligands Protein-protein interface(s) links
Hydrolase inhibitor/hydrolase PDB id
1ta3
Jmol
Contents
Protein chains
274 a.a. *
301 a.a. *
Ligands
NAG ×2
EDO ×7
Waters ×785
* Residue conservation analysis
PDB id:
1ta3
Name: Hydrolase inhibitor/hydrolase
Title: Crystal structure of xylanase (gh10) in complex with inhibit
Structure: Xylanase inhibitor protein i. Chain: a. Synonym: xip-1. Endo-1,4-beta-xylanase. Chain: b. Synonym: gh10, 34 kda xylanase, 1,4-beta-d-xylan xylanohydr x34. Engineered: yes
Source: Triticum aestivum. Bread wheat. Organism_taxid: 4565. Emericella nidulans. Organism_taxid: 162425. Gene: xlnc. Expressed in: emericella nidulans. Expression_system_taxid: 162425
Biol. unit: Dimer (from PQS)
Resolution:
1.70Å     R-factor:   0.135     R-free:   0.166
Authors: F.Payan,P.Leone,C.Furniss,T.Tahir,A.Durand,S.Porciero,P.Manz G.Williamson,H.J.Gilbert,N.Juge,A.Roussel
Key ref:
F.Payan et al. (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. PubMed id: 15181003 DOI: 10.1074/jbc.M404225200
Date:
19-May-04     Release date:   20-Jul-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8L5C6  (XIP1_WHEAT) -  Xylanase inhibitor protein 1
Seq:
Struc:
304 a.a.
274 a.a.
Protein chain
Pfam   ArchSchema ?
Q00177  (XYNC_EMENI) -  Endo-1,4-beta-xylanase C
Seq:
Struc:
327 a.a.
301 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain B: 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   6 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1074/jbc.M404225200 J Biol Chem 279:36029-36037 (2004)
PubMed id: 15181003  
 
 
The dual nature of the wheat xylanase protein inhibitor XIP-I: structural basis for the inhibition of family 10 and family 11 xylanases.
F.Payan, P.Leone, S.Porciero, C.Furniss, T.Tahir, G.Williamson, A.Durand, P.Manzanares, H.J.Gilbert, N.Juge, A.Roussel.
 
  ABSTRACT  
 
The xylanase inhibitor protein I (XIP-I) from wheat Triticum aestivum is the prototype of a novel class of cereal protein inhibitors that inhibit fungal xylanases belonging to glycoside hydrolase families 10 (GH10) and 11 (GH11). The crystal structures of XIP-I in complex with Aspergillus nidulans (GH10) and Penicillium funiculosum (GH11) xylanases have been solved at 1.7 and 2.5 A resolution, respectively. The inhibition strategy is novel because XIP-I possesses two independent enzyme-binding sites, allowing binding to two glycoside hydrolases that display a different fold. Inhibition of the GH11 xylanase is mediated by the insertion of an XIP-I Pi-shaped loop (Lalpha(4)beta(5)) into the enzyme active site, whereas residues in the helix alpha7 of XIP-I, pointing into the four central active site subsites, are mainly responsible for the reversible inactivation of GH10 xylanases. The XIP-I strategy for inhibition of xylanases involves substrate-mimetic contacts and interactions occluding the active site. The structural determinants of XIP-I specificity demonstrate that the inhibitor is able to interact with GH10 and GH11 xylanases of both fungal and bacterial origin. The biological role of the xylanase inhibitors is discussed in light of the present structural data.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. A, structure of the XIP-I-XLNC complex. XIP-I is in red and blue, and A. nidulans xylanase (XLNC) is in purple and green. The main interaction residues are shown in a stick representation, Lys-234[XIP-I] side chain (dark blue) is important for the interaction with XLNC, and Arg-149[XIP-I] (light blue) is important for the interaction with XYNC (B), together with the side chains of the two catalytic residues (red). B, structure of the XIP-I-XYNC complex. XIP-I is in red and blue, and P. funiculosum xylanase (XYNC) is in purple and green. The long inhibitor loop interacting directly in the xylanase active site is shown. The main interaction residues are shown in a stick representation, Arg-149[XIP-I] side chain (dark blue) is important for the interaction with XYNC, and Lys-234[XIP-I] (light blue) is important for the interaction with XLNC (see A), together with the side chains of the two catalytic residues (red). Figures were generated by SPOCK (36).
Figure 2.
FIG. 2. A, structural basis for the inhibition of GH10 xylanase XLNC. The molecular surface of XLNC is shown in gray. Enzyme surfaces (and corresponding residues numbering) interacting with XIP-I are depicted in purple, blue, and green. The known substrate subsites are labeled. Inhibitor residues interacting in the active site groove are shown in a stick representation (colored according to the atom type). Regions from the inhibitor molecule involved in the inhibiting mechanism are represented by red tubes (residue numbering in parentheses). B, structural basis for the inhibition of GH11 xylanase XYNC. A close up of the XYNC active site is the same as in A. Figures were prepared with SPOCK (36).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 36029-36037) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21299880 E.A.Vasconcelos, C.G.Santana, C.V.Godoy, C.D.Seixas, M.S.Silva, L.R.Moreira, O.B.Oliveira-Neto, D.Price, E.Fitches, E.X.Filho, A.Mehta, J.A.Gatehouse, and M.F.Grossi-De-Sa (2011).
A new chitinase-like xylanase inhibitor protein (XIP) from coffee (Coffea arabica) affects Soybean Asian rust (Phakopsora pachyrhizi) spore germination.
  BMC Biotechnol, 11, 14.  
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
  20944220 P.J.Turnbaugh, B.Henrissat, and J.I.Gordon (2010).
Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1261-1264.  
21092126 S.Kumar, N.Singh, B.Mishra, D.Dube, M.Sinha, S.B.Singh, S.Dey, P.Kaur, S.Sharma, and T.P.Singh (2010).
Modulation of inhibitory activity of xylanase-α-amylase inhibitor protein (XAIP): binding studies and crystal structure determination of XAIP-II from Scadoxus multiflorus at 1.2 Å resolution.
  BMC Struct Biol, 10, 41.
PDB code: 3mu7
20528916 S.Kumar, N.Singh, M.Sinha, D.Dube, S.B.Singh, A.Bhushan, P.Kaur, A.Srinivasan, S.Sharma, and T.P.Singh (2010).
Crystal structure determination and inhibition studies of a novel xylanase and alpha-amylase inhibitor protein (XAIP) from Scadoxus multiflorus.
  FEBS J, 277, 2868-2882.
PDB codes: 3hu7 3m7s
20066263 T.M.Gloster, and G.J.Davies (2010).
Glycosidase inhibition: assessing mimicry of the transition state.
  Org Biomol Chem, 8, 305-320.  
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.  
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.  
18384043 G.André-Leroux, J.G.Berrin, J.Georis, F.Arnaut, and N.Juge (2008).
Structure-based mutagenesis of Penicillium griseofulvum xylanase using computational design.
  Proteins, 72, 1298-1307.  
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.  
18511458 T.Tokunaga, Y.Miyata, Y.Fujikawa, and M.Esaka (2008).
RNAi-mediated knockdown of the XIP-type endoxylanase inhibitor gene, OsXIP, has no effect on grain development and germination in rice.
  Plant Cell Physiol, 49, 1122-1127.  
17216454 J.G.Berrin, e.l. .H.Ajandouz, J.Georis, F.Arnaut, and N.Juge (2007).
Substrate and product hydrolysis specificity in family 11 glycoside hydrolases: an analysis of Penicillium funiculosum and Penicillium griseofulvum xylanases.
  Appl Microbiol Biotechnol, 74, 1001-1010.  
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.  
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
16652352 M.Kozak (2006).
Solution scattering studies of conformation stability of xylanase XYNII from Trichoderma longibrachiatum.
  Biopolymers, 83, 95.  
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.  
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.  
15794761 A.Durand, R.Hughes, A.Roussel, R.Flatman, B.Henrissat, and N.Juge (2005).
Emergence of a subfamily of xylanase inhibitors within glycoside hydrolase family 18.
  FEBS J, 272, 1745-1755.  
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.  
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.  
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.