6L77

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.219
R-Value Work: 0.174
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.13817
Primary Citation of 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.

Organizational Affiliation

National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A193DU83
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.174
R-Value Observed: 0.176
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-06-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-06-03
Type: Initial release
Version 1.1: 2020-12-09
Changes: Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.