6JRG

Crystal structure of ZmMoc1 H253A mutant in complex with Holliday junction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.005 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of sequence-specific Holliday junction cleavage by MOC1.

Lin, H.Zhang, D.Zuo, K.Yuan, C.Li, J.Huang, M.Lin, Z.

(2019) Nat.Chem.Biol. --: --

  • DOI: 10.1038/s41589-019-0377-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Holliday junction (HJ) is a key intermediate during homologous recombination and DNA double-strand break repair. Timely HJ resolution by resolvases is critical for maintaining genome stability. The mechanisms underlying sequence-specific substrat ...

    The Holliday junction (HJ) is a key intermediate during homologous recombination and DNA double-strand break repair. Timely HJ resolution by resolvases is critical for maintaining genome stability. The mechanisms underlying sequence-specific substrate recognition and cleavage by resolvases remain elusive. The monokaryotic chloroplast 1 protein (MOC1) specifically cleaves four-way DNA junctions in a sequence-specific manner. Here, we report the crystal structures of MOC1 from Zea mays, alone or bound to HJ DNA. MOC1 uses a unique β-hairpin to embrace the DNA junction. A base-recognition motif specifically interacts with the junction center, inducing base flipping and pseudobase-pair formation at the strand-exchanging points. Structures of MOC1 bound to HJ and different metal ions support a two-metal ion catalysis mechanism. Further molecular dynamics simulations and biochemical analyses reveal a communication between specific substrate recognition and metal ion-dependent catalysis. Our study thus provides a mechanism for how a resolvase turns substrate specificity into catalytic efficiency.


    Organizational Affiliation

    College of Biological Science and Engineering, Fuzhou University, Fuzhou, China.,College of Chemistry, Fuzhou University, Fuzhou, China. Zhonghui.lin@fzu.edu.cn.,College of Chemistry, Fuzhou University, Fuzhou, China. hmd_lab@fzu.edu.cn.,College of Chemistry, Fuzhou University, Fuzhou, China.,College of Chemistry, Fuzhou University, Fuzhou, China. J.li@fzu.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Monokaryotic chloroplast 1
A, B
174Zea maysMutation(s): 1 
Gene Names: 100192759
Find proteins for B4FCI7 (Zea mays)
Go to UniProtKB:  B4FCI7
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (33-MER)C33synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (32-MER)D33synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.005 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.572α = 90.00
b = 77.841β = 97.93
c = 63.854γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-10-30
    Type: Data collection, Database references