6L77 | pdb_00006l77

Crystal structure of MS5 from Brassica napus

• PDB DOI: https://doi.org/10.2210/pdb6L77/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Brassica napus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-31 Released: 2020-06-03 
• Deposition Author(s): Wang, X., Guan, Z.Y., Yin, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Structural analysis of the meiosis-related protein MS5 reveals non-canonical papain enhancement by cystatin-like folds.

Wang, X., Gao, Y., Guan, Z., Xie, Z., Zhang, D., Yin, P., Yang, G., Hong, D., Xin, Q.

(2020) FEBS Lett 594: 2462-2471

• PubMed: 32415887 
• DOI: https://doi.org/10.1002/1873-3468.13817
• Primary Citation Related Structures: 
  6L77


• PubMed Abstract: 
  

  MS5 is a meiosis-related protein belonging to the Brassicaceae-specific domain of unknown function family and characterized by the MS5 superfamily domain (MSD). In this study, we elucidated the three-dimensional crystal structure and potential biochemical function of the MSD. It was observed that the MSD adopts a cystatin-like fold, mainly consisting of a central α-helix and four- or five-stranded antiparallel β-sheets that wrap around it. However, unlike cystatins, which inhibit cysteine proteases, the MSD displayed allosteric activation of papain. We believe that our study provides insight into novel mechanisms of proteolytic enzyme regulation and may serve as a basis for functional studies of the MS5 family proteins in plants.

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Organizational Affiliation: 
• National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 28.49 kDa 
• Atom Count: 1,939 
• Modeled Residue Count: 214 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MS5a	A	242	Brassica napus	Mutation(s): 0  Gene Names: MS5
UniProt
Find proteins for A0A193DU83 (Brassica napus) Explore A0A193DU83  Go to UniProtKB:  A0A193DU83

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.672	α = 90
b = 52.672	β = 90
c = 168.424	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Wang, X., Guan, Z.Y., Yin, P.

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2020-12-09
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary