5HXY

Crystal structure of XerA recombinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of Thermoplasma acidophilum XerA recombinase shows large C-shape clamp conformation and cis-cleavage mode for nucleophilic tyrosine

Jo, C.H.Kim, J.Han, A.R.Park, S.Y.Hwang, K.Y.Nam, K.H.

(2016) FEBS Lett 590: 848-856

  • DOI: 10.1002/1873-3468.12109
  • Primary Citation of Related Structures:  
    5HXY

  • PubMed Abstract: 
  • Site-specific Xer recombination plays a pivotal role in reshuffling genetic information. Here, we report the 2.5 Å crystal structure of XerA from the archaean Thermoplasma acidophilum. Crystallographic data reveal a uniquely open conformational state, resulting in a C-shaped clamp with an angle of ~ 48° and a distance of 57 Å between the core-binding and the catalytic domains ...

    Site-specific Xer recombination plays a pivotal role in reshuffling genetic information. Here, we report the 2.5 Å crystal structure of XerA from the archaean Thermoplasma acidophilum. Crystallographic data reveal a uniquely open conformational state, resulting in a C-shaped clamp with an angle of ~ 48° and a distance of 57 Å between the core-binding and the catalytic domains. The catalytic nucleophile, Tyr264, is positioned in cis-cleavage mode by XerA's C-term tail that interacts with the CAT domain of a neighboring monomer without DNA substrate. Structural comparisons of tyrosine recombinases elucidate the dynamics of Xer recombinase.


    Organizational Affiliation

    Pohang Accelerator Laboratory, Pohang University of Science and Technology, Kyungbuk, Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine recombinase XerA
A, B, C, D, E, F
A, B, C, D, E, F
317Thermoplasma acidophilum DSM 1728Mutation(s): 0 
Gene Names: xerATa1314
UniProt
Find proteins for Q9HIM5 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore Q9HIM5 
Go to UniProtKB:  Q9HIM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HIM5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.86α = 90
b = 105.968β = 110.01
c = 115.586γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
SOLVEphasing
RESOLVEmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-01-31 
  • Released Date: 2017-02-01 
  • Deposition Author(s): Hwang, K.Y., Nam, K.H.

Funding OrganizationLocationGrant Number
National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)Korea, Republic OfNRF-2014R1A1A2059440
National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)Korea, Republic OfNRF-2014R1212513

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection