2HCZ

Crystal structure of EXPB1 (Zea m 1), a beta-expansin and group-1 pollen allergen from maize


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure and activities of EXPB1 (Zea m 1), a beta-expansin and group-1 pollen allergen from maize.

Yennawar, N.H.Li, L.C.Dudzinski, D.M.Tabuchi, A.Cosgrove, D.J.

(2006) Proc Natl Acad Sci U S A 103: 14664-14671

  • DOI: 10.1073/pnas.0605979103
  • Structures With Same Primary Citation

  • PubMed 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 indu ...

    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.


    Organizational Affiliation

    Huck Institutes of the Life Sciences and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-expansin 1a
X
245Zea maysMutation(s): 1 
Gene Names: EXPB1EXPB1A
Find proteins for P58738 (Zea mays)
Go to UniProtKB:  P58738
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
X
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
X
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FCA
Query on FCA

Download CCD File 
X
ALPHA-D-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-PHYPRBDBSA-N
 Ligand Interaction
XYS
Query on XYS

Download CCD File 
X
XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
X
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.408α = 90
b = 44.512β = 124.64
c = 69.467γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
DMphasing
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description