6MDW

Mechanism of protease dependent DPC repair


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Insight into DNA-Dependent Activation of Human Metalloprotease Spartan.

Li, F.Raczynska, J.E.Chen, Z.Yu, H.

(2019) Cell Rep 26: 3336-3346.e4

  • DOI: https://doi.org/10.1016/j.celrep.2019.02.082
  • Primary Citation of Related Structures:  
    6MDW, 6MDX

  • PubMed Abstract: 

    The DNA-dependent metalloprotease Spartan (SPRTN) cleaves DNA-protein crosslinks (DPCs) and protects cells from DPC-induced genome instability. Germline mutations of SPRTN are linked to human Ruijs-Aalfs syndrome (RJALS) characterized by progeria and early-onset hepatocellular carcinoma. The mechanism of DNA-mediated activation of SPRTN is not understood. Here, we report the crystal structure of the human SPRTN SprT domain bound to single-stranded DNA (ssDNA). Our structure reveals a Zn 2+ -binding sub-domain (ZBD) in SprT that shields its active site located in the metalloprotease sub-domain (MPD). The narrow catalytic groove between MPD and ZBD only permits cleavage of flexible substrates. The ZBD contains an ssDNA-binding site, with a DNA-base-binding pocket formed by aromatic residues. Mutations of ssDNA-binding residues diminish the protease activity of SPRTN. We propose that the ZBD contributes to the ssDNA specificity of SPRTN, restricts the access of globular substrates, and positions DPCs, which may need to be partially unfolded, for optimal cleavage.


  • Organizational Affiliation

    Department of Pharmacology, Howard Hughes Medical Institute.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SprT-like domain-containing protein Spartan194Homo sapiensMutation(s): 0 
Gene Names: SPRTNC1orf124DVC1UNQ1880/PRO4323
EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H040 (Homo sapiens)
Explore Q9H040 
Go to UniProtKB:  Q9H040
PHAROS:  Q9H040
GTEx:  ENSG00000010072 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H040
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLZ
Query on MLZ
A
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.422α = 90
b = 29.553β = 90
c = 50.242γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)United StatesRP150538-P2

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description