6JRG

Crystal structure of ZmMoc1 H253A mutant in complex with Holliday junction

• PDB DOI:  https://doi.org/10.2210/pdb6JRG/pdb
• NAKB: 6JRG

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Zea mays, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-04-03 Released: 2019-10-23 
• Deposition Author(s): Lin, Z., Lin, H., Zhang, D., Yuan, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.232 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

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 15: 1241-1248

• PubMed: 31611704 
• DOI: https://doi.org/10.1038/s41589-019-0377-4
• Primary Citation of Related Structures:  
  6IS8, 6IS9, 6JRF, 6JRG


• 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 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.

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Organizational Affiliation: 

College of Chemistry, Fuzhou University, Fuzhou, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 57.61 kDa 
• Atom Count: 4,171 
• Modelled Residue Count: 391 
• Deposited Residue Count: 414 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monokaryotic chloroplast 1	A, B	174	Zea mays	Mutation(s): 1  Gene Names: Moc1, 100192759, ZEAMMB73_Zm00001d040409
UniProt
Find proteins for B4FCI7 (Zea mays) Explore B4FCI7  Go to UniProtKB:  B4FCI7

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (33-MER)	C	33	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (32-MER)	D	33	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.232 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.572	α = 90
b = 77.841	β = 97.93
c = 63.854	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-23 
Deposition Author(s): Lin, Z., Lin, H., Zhang, D., Yuan, C.

Revision History  

• Version 1.0: 2019-10-23
  Type: Initial release
  
• Version 1.1: 2019-10-30
  Changes: Data collection, Database references
• Version 1.2: 2019-12-04
  Changes: Database references