8AE5

Crystal structure of human legumain in complex with macrocypin 1a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Structural and functional studies of legumain-mycocypin complexes revealed a competitive, exosite-regulated mode of interaction.

Elamin, T.Santos, N.P.Briza, P.Brandstetter, H.Dall, E.

(2022) J Biol Chem 298: 102502-102502

  • DOI: https://doi.org/10.1016/j.jbc.2022.102502
  • Primary Citation of Related Structures:  
    8AE4, 8AE5

  • PubMed Abstract: 

    Under pathophysiologic conditions such as Alzheimer's disease and cancer, the endolysosomal cysteine protease legumain was found to translocate to the cytosol, the nucleus, and the extracellular space. These noncanonical localizations demand for a tight regulation of legumain activity, which is in part conferred by protein inhibitors. While there is a significant body of knowledge on the interaction of human legumain with endogenous cystatins, only little is known on its regulation by fungal mycocypins. Mycocypins are characterized by (i) versatile, plastic surface loops allowing them to inhibit different classes of enzymes and (ii) a high resistance toward extremes of pH and temperature. These properties make mycocypins attractive starting points for biotechnological and medical applications. In this study, we show that mycocypins utilize an adaptable reactive center loop to target the active site of legumain in a substrate-like manner. The interaction was further stabilized by variable, isoform-specific exosites, converting the substrate recognition into inhibition. Additionally, we found that selected mycocypins were capable of covalent complex formation with legumain by forming a disulfide bond to the active site cysteine. Furthermore, our inhibition studies with other clan CD proteases suggested that mycocypins may serve as broad-spectrum inhibitors of clan CD proteases. Our studies uncovered the potential of mycocypins as a new scaffold for drug development, providing the basis for the design of specific legumain inhibitors.


  • Organizational Affiliation

    Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LegumainA,
C [auth B]
263Homo sapiensMutation(s): 1 
Gene Names: LGMNPRSC1
EC: 3.4.22.34
UniProt & NIH Common Fund Data Resources
Find proteins for Q99538 (Homo sapiens)
Explore Q99538 
Go to UniProtKB:  Q99538
PHAROS:  Q99538
GTEx:  ENSG00000100600 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99538
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q99538-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Macrocypin-1aB [auth C],
D
177Macrolepiota proceraMutation(s): 0 
UniProt
Find proteins for B9V973 (Macrolepiota procera)
Explore B9V973 
Go to UniProtKB:  B9V973
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9V973
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B],
K [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
I [auth C],
L [auth B],
M [auth D],
N [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SCH
Query on SCH
A,
C [auth B]
L-PEPTIDE LINKINGC4 H9 N O2 S2CYS
SNN
Query on SNN
A,
C [auth B]
L-PEPTIDE LINKINGC4 H6 N2 O2ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.178α = 90
b = 174.122β = 90
c = 112.998γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaP31867

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2022-11-09
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-01-31
    Changes: Refinement description