4YN3

Crystal structure of Cucumisin complex with pro-peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of cucumisin protease activity regulation by its propeptide

Sotokawauchi, A.Kato-Murayama, M.Murayama, K.Hosaka, T.Maeda, I.Onjo, M.Ohsawa, N.Kato, D.I.Arima, K.Shirouzu, M.

(2017) J. Biochem. 161: 45-53

  • DOI: 10.1093/jb/mvw053

  • PubMed Abstract: 
  • Cucumisin [EC 3.4.21.25], a subtilisin-like serine endopeptidase, was isolated from melon fruit, Cucumis melo L. Mature cucumisin (67 kDa, 621 residues) is produced by removal of the propeptide (10 kDa, 88 residues) from the cucumisin precursor by su ...

    Cucumisin [EC 3.4.21.25], a subtilisin-like serine endopeptidase, was isolated from melon fruit, Cucumis melo L. Mature cucumisin (67 kDa, 621 residues) is produced by removal of the propeptide (10 kDa, 88 residues) from the cucumisin precursor by subsequence processing. It is reported that cucumisin is inhibited by its own propeptide. The crystal structure of mature cucumisin is reported to be composed of three domains: the subtilisin-like catalytic domain, the protease-associated domain and the C-terminal fibronectin-III-like domain. In this study, the crystal structure of the mature cucumisin•propeptide complex was determined by the molecular replacement method and refined at 1.95 Å resolution. In this complex, the propeptide had a domain of the α-β sandwich motif with four-stranded antiparallel β-sheets, two helices and a strand of the C-terminal region. The β-sheets of the propeptide bind to two parallel surface helices of cucumisin through hydrophobic interaction and 27 hydrogen bonds. The C-terminus of the propeptide binds to the cleft of the active site as peptide substrates. The inhibitory assay suggested that the C-terminal seven residues of the propeptide do not inhibit the cucumisin activity. The crystal structure of the cucumisin•propeptide complex revealed the regulation mechanism of cucumisin activity.


    Organizational Affiliation

    Department of Chemistry and Bioscience, Faculty of Science, Kagoshima University Graduate School of Science and Engineering, Kagoshima 890-0065, Japan.,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.,Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Sendai 980-8575, Japan.,Experimental Farm, Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan.,Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka 820-8502, Japan.,Department of Chemistry and Bioscience, Faculty of Science, Kagoshima University Graduate School of Science and Engineering, Kagoshima 890-0065, Japan arima@sci.kagoshima-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cucumisin
A
621Cucumis meloMutation(s): 0 
EC: 3.4.21.25
Find proteins for Q39547 (Cucumis melo)
Go to UniProtKB:  Q39547
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cucumisin
B
96Cucumis meloMutation(s): 0 
EC: 3.4.21.25
Find proteins for Q39547 (Cucumis melo)
Go to UniProtKB:  Q39547
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 
  • Space Group: P 42
Unit Cell:
Length (Å)Angle (°)
a = 97.738α = 90.00
b = 97.738β = 90.00
c = 73.433γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-16
    Type: Derived calculations
  • Version 1.2: 2018-11-07
    Type: Data collection, Database references, Derived calculations