5T9J | pdb_00005t9j

Crystal Structure of human GEN1 in complex with Holliday junction DNA in the upper interface

PDB DOI: https://doi.org/10.2210/pdb5T9J/pdb
NAKB: 5T9J

Classification: HYDROLASE
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-09-09 Released: 2016-09-21
Deposition Author(s): Lee, S.-H., Biertumpfel, C.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.241 (Depositor), 0.248 (DCC)
R-Value Work:
0.199 (Depositor), 0.204 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Human Holliday junction resolvase GEN1 uses a chromodomain for efficient DNA recognition and cleavage.

Lee, S.H., Princz, L.N., Klugel, M.F., Habermann, B., Pfander, B., Biertumpfel, C.

(2015) Elife 4

PubMed: 26682650 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.12256
Primary Citation Related Structures:
5T9J

PubMed Abstract:
Holliday junctions (HJs) are key DNA intermediates in homologous recombination. They link homologous DNA strands and have to be faithfully removed for proper DNA segregation and genome integrity. Here, we present the crystal structure of human HJ resolvase GEN1 complexed with DNA at 3.0 Å resolution. The GEN1 core is similar to other Rad2/XPG nucleases. However, unlike other members of the superfamily, GEN1 contains a chromodomain as an additional DNA interaction site. Chromodomains are known for their chromatin-targeting function in chromatin remodelers and histone(de)acetylases but they have not previously been found in nucleases. The GEN1 chromodomain directly contacts DNA and its truncation severely hampers GEN1's catalytic activity. Structure-guided mutations in vitro and in vivo in yeast validated our mechanistic findings. Our study provides the missing structure in the Rad2/XPG family and insights how a well-conserved nuclease core acquires versatility in recognizing diverse substrates for DNA repair and maintenance.

Organizational Affiliation

Department of Structural Cell Biology, Molecular Mechanisms of DNA Repair, Max Planck Institute of Biochemistry, Martinsried, Germany.

Macromolecule Content

Total Structure Weight: 142.76 kDa
Atom Count: 8,002
Modeled Residue Count: 859
Deposited Residue Count: 1,092
Unique protein chains: 1
Unique nucleic acid chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flap endonuclease GEN homolog 1	A, B	506	Homo sapiens	Mutation(s): 3 Gene Names: GEN1 EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q17RS7 (Homo sapiens) Explore Q17RS7 Go to UniProtKB: Q17RS7
PHAROS: Q17RS7 GTEx: ENSG00000178295
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q17RS7
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(DGPDAPDAPDTPDTPDCPDCPDGPDGPDAPDTPDTPDAPDGPDGPDGPDAPDTPDGPDC)-3')	C	20	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
DNA (5'-D(DGPDCPDAPDTPDCPDCPDCPDTPDAPDAPDGPDCPDTPDCPDCPDAPDTPDCPDGPDT)-3')	D	20	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
DNA (5'-D(DAPDCPDGPDAPDTPDGPDGPDAPDGPDCPDCPDGPDCPDTPDAPDGPDGPDCPDTPDC)-3')	E	20	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 5
DNA (5'-D(DGPDAPDGPDCPDCPDTPDAPDGPDCPDGPDTPDCPDCPDGPDGPDAPDAPDTPDTPDC)-3')	F	20	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], U [auth C], V [auth C], W [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		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 A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] 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 A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain T [auth B] MOL2 format, chain N [auth A] MOL2 format, chain T [auth B] mmCIF format, chain N [auth A] mmCIF format, chain T [auth B]	N [auth A], T [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain T [auth B] Interactions & Density Focus chain N [auth A] Focus chain T [auth B]