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PDBsum entry 2hcz

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Allergen PDB id
2hcz
Jmol
Contents
Protein chain
242 a.a. *
Ligands
NAG-NAG-MAN-MAN-
XYS-MAN-FCA
Waters ×17
* Residue conservation analysis
PDB id:
2hcz
Name: Allergen
Title: Crystal structure of expb1 (zea m 1), a beta-expansin and gr pollen allergen from maize
Structure: Beta-expansin 1a. Chain: x. Synonym: pollen allergen zea m 1, zea m i
Source: Zea mays. Organism_taxid: 4577. Tissue: pollen
Resolution:
2.75Å     R-factor:   0.233     R-free:   0.290
Authors: N.H.Yennawar,D.J.Cosgrove
Key ref:
N.H.Yennawar et al. (2006). Crystal structure and activities of EXPB1 (Zea m 1), a beta-expansin and group-1 pollen allergen from maize. Proc Natl Acad Sci U S A, 103, 14664-14671. PubMed id: 16984999 DOI: 10.1073/pnas.0605979103
Date:
19-Jun-06     Release date:   22-Aug-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P58738  (EXPB1_MAIZE) -  Expansin-B1
Seq:
Struc:
269 a.a.
242 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     cell wall organization   2 terms 

 

 
DOI no: 10.1073/pnas.0605979103 Proc Natl Acad Sci U S A 103:14664-14671 (2006)
PubMed id: 16984999  
 
 
Crystal structure and activities of EXPB1 (Zea m 1), a beta-expansin and group-1 pollen allergen from maize.
N.H.Yennawar, L.C.Li, D.M.Dudzinski, A.Tabuchi, D.J.Cosgrove.
 
  ABSTRACT  
 
Expansins are small extracellular proteins that promote turgor-driven extension of plant cell walls. EXPB1 (also called Zea m 1) is a member of the beta-expansin subfamily known in the allergen literature as group-1 grass pollen allergens. EXPB1 induces extension and stress relaxation of grass cell walls. To help elucidate expansin's mechanism of wall loosening, we determined the structure of EXPB1 by x-ray crystallography to 2.75-A resolution. EXPB1 consists of two domains closely packed and aligned so as to form a long, shallow groove with potential to bind a glycan backbone of approximately 10 sugar residues. The structure of EXPB1 domain 1 resembles that of family-45 glycoside hydrolase (GH45), with conservation of most of the residues in the catalytic site. However, EXPB1 lacks a second aspartate that serves as the catalytic base required for hydrolytic activity in GH45 enzymes. Domain 2 of EXPB1 is an Ig-like beta-sandwich, with aromatic and polar residues that form a potential surface for polysaccharide binding in line with the glycan binding cleft of domain 1. EXPB1 binds to maize cell walls, most strongly to xylans, causing swelling of the cell wall. Tests for hydrolytic activity by EXPB1 with various wall polysaccharides proved negative. Moreover, GH45 enzymes and a GH45-related protein called "swollenin" lacked wall extension activity comparable to that of expansins. We propose a model of expansin action in which EXPB1 facilitates the local movement and stress relaxation of arabinoxylan-cellulose networks within the wall by noncovalent rearrangement of its target.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Structure of EXPB1 (PDB ID code 2HCZ). (A) Ribbon model of EXPB1 showing the overall configuration of the two domains. (B) Superposition of the peptide backbone of EXPB1 D1 (shown entirely in red) with the peptide backbone of Humicola Cel45 (PDB ID code 4ENG), colored green for regions of good alignment with EXPB1 and gray otherwise. The yellow residues indicate cellohexaose from the 4ENG model. (C) Superposition of residues making up the catalytic site of Humicola Cel45 (blue) and corresponding residues of EXPB1 (red). Other conserved acidic residues in this region of EXPB1 are shown in purple. (D) Superposition of EXPB1 D2 (colored) and Phl p 2 (gray), a group-2/3 grass pollen allergen (PDB ID code 1WHO). Coloring scale from best to poorest alignment of peptide backbones is shown at the bottom. (E) Top view of the conserved surface of EXPB1, color-coded to indicate conservation (red, most conserved; blue, least conserved; white, intermediate). Conserved residues are labeled, and the locations of two antigenic epitopes are indicated (SITE-D and SITE-A). (F) A model of glucurono-arabinoxylan (yellow and red) was manually fitted to the long open groove of EXPB1 by using the program O (66) and subsequently energy-minimized by using the program CNS (67). Green residues are from D1, cyan residues are from D2, and red residues are the conserved residues identified in E. (G) End view of same model as in F. The image in E was generated from the program CONSURF (68) by using the alignment of 80 EXPB proteins in the GenBank database and 2HCZ after removal of the N-terminal extension. The images in G and F were generated with PYMOL (DeLano Scientific) after removal of the N-terminal extension.
Figure 3.
Fig. 3. EXPB sequence logo based on 80 EXPB proteins from the GenBank database, aligned with the sequence of maize EXPB1 (green) and color-coded to indicate the structural role of the conserved residues. Residues with unspecified roles are shown in gray. The size of the one-letter amino acid code in the sequence logo indicates the degree of conservation on a logarithmic scale. The logo was generated with WebLogo (http://weblogo.berkeley.edu). Black lines between Cys residues indicate disulfide bonds.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20981266 C.H.Schein, O.Ivanciuc, T.Midoro-Horiuti, R.M.Goldblum, and W.Braun (2010).
An Allergen Portrait Gallery: Representative Structures and an Overview of IgE Binding Surfaces.
  Bioinform Biol Insights, 4, 113-125.  
20213317 H.J.Lee, S.Lee, H.J.Ko, K.H.Kim, and I.G.Choi (2010).
An expansin-like protein from Hahella chejuensis binds cellulose and enhances cellulase activity.
  Mol Cells, 29, 379-385.  
20507562 J.Breen, D.Li, D.S.Dunn, F.Békés, X.Kong, J.Zhang, J.Jia, T.Wicker, R.Mago, W.Ma, M.Bellgard, and R.Appels (2010).
Wheat beta-expansin (EXPB11) genes: Identification of the expressed gene on chromosome 3BS carrying a pollen allergen domain.
  BMC Plant Biol, 10, 99.  
20178562 V.Arantes, and J.N.Saddler (2010).
Access to cellulose limits the efficiency of enzymatic hydrolysis: the role of amorphogenesis.
  Biotechnol Biofuels, 3, 4.  
19058186 E.S.Kim, H.J.Lee, W.G.Bang, I.G.Choi, and K.H.Kim (2009).
Functional characterization of a bacterial expansin from Bacillus subtilis for enhanced enzymatic hydrolysis of cellulose.
  Biotechnol Bioeng, 102, 1342-1353.  
19048286 H.Mélida, P.García-Angulo, A.Alonso-Simón, A.Encina, J.Alvarez, and J.L.Acebes (2009).
Novel type II cell wall architecture in dichlobenil-habituated maize calluses.
  Planta, 229, 617-631.  
18682111 A.Pomés (2008).
Allergen structures and biologic functions: the cutting edge of allergy research.
  Curr Allergy Asthma Rep, 8, 425-432.  
17660182 D.S.Thompson (2008).
Space and time in the plant cell wall: relationships between cell type, cell wall rheology and cell function.
  Ann Bot (Lond), 101, 203-211.  
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.  
18971341 F.Kerff, A.Amoroso, R.Herman, E.Sauvage, S.Petrella, P.Filée, P.Charlier, B.Joris, A.Tabuchi, N.Nikolaidis, and D.J.Cosgrove (2008).
Crystal structure and activity of Bacillus subtilis YoaJ (EXLX1), a bacterial expansin that promotes root colonization.
  Proc Natl Acad Sci U S A, 105, 16876-16881.
PDB codes: 2bh0 3d30
18547393 H.O.Ghiglione, F.G.Gonzalez, R.Serrago, S.B.Maldonado, C.Chilcott, J.A.Curá, D.J.Miralles, T.Zhu, and J.J.Casal (2008).
Autophagy regulated by day length determines the number of fertile florets in wheat.
  Plant J, 55, 1010-1024.  
18487988 M.B.Sticklen (2008).
Plant genetic engineering for biofuel production: towards affordable cellulosic ethanol.
  Nat Rev Genet, 9, 433-443.  
18275468 S.Fudali, S.Janakowski, M.Sobczak, M.Griesser, F.M.Grundler, and W.Golinowski (2008).
Two tomato alpha-expansins show distinct spatial and temporal expression patterns during development of nematode-induced syncytia.
  Physiol Plant, 132, 370-383.  
17003114 T.H.Davis, and D.J.Cosgrove (2006).
Profile of Daniel J. Cosgrove.
  Proc Natl Acad Sci U S A, 103, 14661-14663.  
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.