2XQR

Crystal structure of plant cell wall invertase in complex with a specific protein inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Insights Into the Ph-Controlled Targeting of Plant Cell-Wall Invertase by a Specific Inhibitor Protein.

Hothorn, M.Van Den Ende, W.Lammens, W.Rybin, V.Scheffzek, K.

(2010) Proc.Natl.Acad.Sci.USA 107: 17427

  • DOI: 10.1073/pnas.1004481107

  • PubMed Abstract: 
  • Invertases are highly regulated enzymes with essential functions in carbohydrate partitioning, sugar signaling, and plant development. Here we present the 2.6 Å crystal structure of Arabidopsis cell-wall invertase 1 (INV1) in complex with a protein i ...

    Invertases are highly regulated enzymes with essential functions in carbohydrate partitioning, sugar signaling, and plant development. Here we present the 2.6 Å crystal structure of Arabidopsis cell-wall invertase 1 (INV1) in complex with a protein inhibitor (CIF, or cell-wall inhibitor of β-fructosidase) from tobacco. The structure identifies a small amino acid motif in CIF that directly targets the invertase active site. The activity of INV1 and its interaction with CIF are strictly pH-dependent with a maximum at about pH 4.5. At this pH, isothermal titration calorimetry reveals that CIF tightly binds its target with nanomolar affinity. CIF competes with sucrose (Suc) for the same binding site, suggesting that both the extracellular Suc concentration and the pH changes regulate association of the complex. A conserved glutamate residue in the complex interface was previously identified as an important quantitative trait locus affecting fruit quality, which implicates the invertase-inhibitor complex as a main regulator of carbon partitioning in plants. Comparison of the CIF/INV1 structure with the complex between the structurally CIF-related pectin methylesterase inhibitor (PMEI) and pectin methylesterase indicates a common targeting mechanism in PMEI and CIF. However, CIF and PMEI use distinct surface areas to selectively inhibit very different enzymatic scaffolds.


    Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
A, C, E, G, I, K
537Arabidopsis thalianaMutation(s): 0 
Gene Names: CWINV1 (BFRUCT1)
EC: 3.2.1.26
Find proteins for Q43866 (Arabidopsis thaliana)
Go to UniProtKB:  Q43866
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INVERTASE INHIBITOR
B, D, F, H, J, L
149Nicotiana tabacumMutation(s): 0 
Gene Names: LOC107808322
Find proteins for O49908 (Nicotiana tabacum)
Go to UniProtKB:  O49908
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

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Download CCD File 
B, D, F, H, J, L
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B, C, E, G, I, K
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FRU
Query on FRU

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Download CCD File 
A, C, E, G, I, K
FRUCTOSE
C6 H12 O6
RFSUNEUAIZKAJO-ARQDHWQXSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A, C, E, G, I, K
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, C, E, G, I, K
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, C, E, G, I, K
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 199.980α = 90.00
b = 199.980β = 90.00
c = 111.160γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-06-09
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-07
    Type: Source and taxonomy