6LCT

Crystal structure of catalytic inactive chloroplast resolvase NtMOC1 in complex with Holliday junction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

wwPDB Validation 3D Report Full Report



Literature

Structural insights into sequence-dependent Holliday junction resolution by the chloroplast resolvase MOC1.

Yan, J.Hong, S.Guan, Z.He, W.Zhang, D.Yin, P.

(2020) Nat Commun 11: 1417-1417

  • DOI: 10.1038/s41467-020-15242-8
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Holliday junctions (HJs) are key DNA intermediates in genetic recombination and are eliminated by nuclease, termed resolvase, to ensure genome stability. HJ resolvases have been identified across all kingdoms of life, members of which exhibit sequenc ...

    Holliday junctions (HJs) are key DNA intermediates in genetic recombination and are eliminated by nuclease, termed resolvase, to ensure genome stability. HJ resolvases have been identified across all kingdoms of life, members of which exhibit sequence-dependent HJ resolution. However, the molecular basis of sequence selectivity remains largely unknown. Here, we present the chloroplast resolvase MOC1, which cleaves HJ in a cytosine-dependent manner. We determine the crystal structure of MOC1 with and without HJs. MOC1 exhibits an RNase H fold, belonging to the retroviral integrase family. MOC1 functions as a dimer, and the HJ is embedded into the basic cleft of the dimeric enzyme. We characterize a base recognition loop (BR loop) that protrudes into and opens the junction. Residues from the BR loop intercalate into the bases, disrupt the C-G base pairing at the crossover and recognize the cytosine, providing the molecular basis for sequence-dependent HJ resolution by a resolvase.


    Organizational Affiliation

    National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China. yinping@mail.hzau.edu.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NtMOC1
A, B
169Nicotiana tabacumMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*AP*AP*CP*AP*GP*AP*GP*GP*AP*TP*GP*GP*AP*GP*CP*T)-3')C18synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*CP*TP*TP*GP*CP*TP*GP*GP*GP*AP*CP*AP*TP*CP*TP*T)-3')D18synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*GP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*CP*AP*AP*GP*GP*C)-3')E18synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*GP*AP*TP*GP*TP*CP*CP*CP*TP*CP*TP*GP*TP*TP*GP*T)-3')F18synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.054α = 90
b = 89.807β = 90
c = 68.478γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-04-08
    Type: Initial release