2XQR | pdb_00002xqr

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 (Depositor), 0.189 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 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 U S A 107: 17427

  • DOI: https://doi.org/10.1073/pnas.1004481107
  • Primary Citation Related Structures: 
    2XQR

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 475.51 kDa 
  • Atom Count: 34,132 
  • Modeled Residue Count: 4,098 
  • Deposited Residue Count: 4,116 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
A, C, E, G, I
A, C, E, G, I, K
537Arabidopsis thalianaMutation(s): 0 
EC: 3.2.1.26
UniProt
Find proteins for Q43866 (Arabidopsis thaliana)
Explore Q43866 
Go to UniProtKB:  Q43866
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ43866
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
INVERTASE INHIBITOR
B, D, F, H, J
B, D, F, H, J, L
149Nicotiana tabacumMutation(s): 0 
UniProt
Find proteins for O49908 (Nicotiana tabacum)
Explore O49908 
Go to UniProtKB:  O49908
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO49908
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M, O, Q, S, U
M, O, Q, S, U, W
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G89333WS
GlyCosmos: G89333WS
GlyGen: G89333WS
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N, P, R, T, V
N, P, R, T, V, X
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE

Query on EPE



Download:Ideal Coordinates CCD File
BA [auth B]
GA [auth D]
KA [auth F]
OA [auth H]
SA [auth J]
BA [auth B],
GA [auth D],
KA [auth F],
OA [auth H],
SA [auth J],
WA [auth L]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth A]
FA [auth C]
JA [auth E]
NA [auth G]
RA [auth I]
AA [auth A],
FA [auth C],
JA [auth E],
NA [auth G],
RA [auth I],
VA [auth K]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FRU

Query on FRU



Download:Ideal Coordinates CCD File
DA [auth C]
HA [auth E]
LA [auth G]
PA [auth I]
TA [auth K]
DA [auth C],
HA [auth E],
LA [auth G],
PA [auth I],
TA [auth K],
Y [auth A]
beta-D-fructofuranose
C6 H12 O6
RFSUNEUAIZKAJO-ARQDHWQXSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
CA [auth B]
EA [auth C]
IA [auth E]
MA [auth G]
QA [auth I]
CA [auth B],
EA [auth C],
IA [auth E],
MA [auth G],
QA [auth I],
UA [auth K],
Z [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free:  0.210 (Depositor), 0.189 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 199.98α = 90
b = 199.98β = 90
c = 111.16γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-06-09
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Structure summary