5HXY | pdb_00005hxy

Crystal structure of XerA recombinase

PDB DOI: https://doi.org/10.2210/pdb5HXY/pdb

Classification: RECOMBINATION
Organism(s): Thermoplasma acidophilum DSM 1728
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-01-31 Released: 2017-02-01
Deposition Author(s): Hwang, K.Y., Nam, K.H.
Funding Organization(s): National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.243 (Depositor), 0.210 (DCC)
R-Value Work:
0.188 (Depositor)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 26919387 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.12109
Primary Citation 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. 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

Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea.

Macromolecule Content

Total Structure Weight: 223.7 kDa
Atom Count: 14,067
Modeled Residue Count: 1,654
Deposited Residue Count: 1,902
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine recombinase XerA	A, B, C, D, E A, B, C, D, E, F	317	Thermoplasma acidophilum DSM 1728	Mutation(s): 0 Gene Names: xerA, Ta1314
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HIM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain U [auth F] SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain U [auth F] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain U [auth F] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth B] G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth C], P [auth D], Q [auth D], R [auth E], S [auth E], T [auth F], U [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.243 (Depositor), 0.210 (DCC)
R-Value Work: 0.188 (Depositor)
R-Value Observed: 0.191 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.86	α = 90
b = 105.968	β = 110.01
c = 115.586	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
SOLVE	phasing
RESOLVE	model building
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-02-01

Deposition Author(s):

Hwang, K.Y.

Nam, K.H.

Funding Organization	Location	Grant Number
National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)	Korea, Republic Of	NRF-2014R1A1A2059440
National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)	Korea, Republic Of	NRF-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
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Structure summary