7S5F

Crystal structure of mannose-6-phosphate reductase from celery (Apium graveolens) leaves with NADP+ and mannonic acid bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural Determinants of Sugar Alcohol Biosynthesis in Plants: The Crystal Structures of Mannose-6-Phosphate and Aldose-6-Phosphate Reductases.

Minen, R.I.Bhayani, J.A.Hartman, M.D.Cereijo, A.E.Zheng, Y.Ballicora, M.A.Iglesias, A.A.Liu, D.Figueroa, C.M.

(2022) Plant Cell Physiol 63: 658-670

  • DOI: https://doi.org/10.1093/pcp/pcac029
  • Primary Citation of Related Structures:  
    7S5F, 7S5I

  • PubMed Abstract: 

    Sugar alcohols are major photosynthetic products in plant species from the Apiaceae and Plantaginaceae families. Mannose-6-phosphate reductase (Man6PRase) and aldose-6-phosphate reductase (Ald6PRase) are key enzymes for synthesizing mannitol and glucitol in celery (Apium graveolens) and peach (Prunus persica), respectively. In this work, we report the first crystal structures of dimeric plant aldo/keto reductases (AKRs), celery Man6PRase (solved in the presence of mannonic acid and NADP+) and peach Ald6PRase (obtained in the apo form). Both structures displayed the typical TIM barrel folding commonly observed in proteins from the AKR superfamily. Analysis of the Man6PRase holo form showed that residues putatively involved in the catalytic mechanism are located close to the nicotinamide ring of NADP+, where the hydride transfer to the sugar phosphate should take place. Additionally, we found that Lys48 is important for the binding of the sugar phosphate. Interestingly, the Man6PRase K48A mutant had a lower catalytic efficiency with mannose-6-phosphate but a higher catalytic efficiency with mannose than the wild type. Overall, our work sheds light on the structure-function relationships of important enzymes to synthesize sugar alcohols in plants.


  • Organizational Affiliation

    UNL, CONICET, FBCB, Instituto de Agrobiotecnología del Litoral, UNL, CONICET, FBCB, Santa Fe 3000, Argentina.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Manose-6-phosphate reductaseA [auth B],
B [auth A],
C,
D
309Apium graveolensMutation(s): 0 
Gene Names: M6PR
UniProt
Find proteins for A0A1U9WT24 (Apium graveolens)
Explore A0A1U9WT24 
Go to UniProtKB:  A0A1U9WT24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1U9WT24
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
E [auth B],
G [auth A],
I [auth C],
K [auth D]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
CS2 (Subject of Investigation/LOI)
Query on CS2

Download Ideal Coordinates CCD File 
F [auth B],
H [auth A],
J [auth C],
L [auth D]
D-MANNONIC ACID
C6 H12 O7
RGHNJXZEOKUKBD-MBMOQRBOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.202α = 90
b = 61.779β = 107.67
c = 148.063γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB 1616851

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2022-03-23
    Changes: Database references
  • Version 1.2: 2022-05-25
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description