6O8E

Crystal structure of UvrB bound to duplex DNA with ADP

PDB DOI: https://doi.org/10.2210/pdb6O8E/pdb
NAKB: 6O8E

Classification: DNA BINDING PROTEIN/DNA
Organism(s): [Bacillus] caldotenax, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-10 Released: 2020-01-22
Deposition Author(s): Lee, S.-J., Verdine, G.L.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.270
R-Value Work: 0.215
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mechanism of DNA Lesion Homing and Recognition by the Uvr Nucleotide Excision Repair System.

Lee, S.J., Sung, R.J., Verdine, G.L.

(2019) Research (Wash D C) 2019: 5641746-5641746

PubMed: 31549070 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.34133/2019/5641746
Primary Citation of Related Structures:
6O8E, 6O8F, 6O8G, 6O8H

PubMed Abstract:
Nucleotide excision repair (NER) is an essential DNA repair system distinguished from other such systems by its extraordinary versatility. NER removes a wide variety of structurally dissimilar lesions having only their bulkiness in common. NER can also repair several less bulky nucleobase lesions, such as 8-oxoguanine. Thus, how a single DNA repair system distinguishes such a diverse array of structurally divergent lesions from undamaged DNA has been one of the great unsolved mysteries in the field of genome maintenance. Here we employ a synthetic crystallography approach to obtain crystal structures of the pivotal NER enzyme UvrB in complex with duplex DNA, trapped at the stage of lesion-recognition. These structures coupled with biochemical studies suggest that UvrB integrates the ATPase-dependent helicase/translocase and lesion-recognition activities. Our work also conclusively establishes the identity of the lesion-containing strand and provides a compelling insight to how UvrB recognizes a diverse array of DNA lesions.

Organizational Affiliation

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.

Macromolecule Content

Total Structure Weight: 162.23 kDa
Atom Count: 11,279
Modelled Residue Count: 1,262
Deposited Residue Count: 1,266
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UvrABC system protein B	A, B	593	[Bacillus] caldotenax	Mutation(s): 0 Gene Names: uvrB
UniProt
Find proteins for P56981 (Bacillus caldotenax) Explore P56981 Go to UniProtKB: P56981
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P56981
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

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

Find similar nucleic acids by: Sequence | 3D Structure

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B]	G [auth A], P [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain P [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth B] MOL2 format, chain H [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth B]	H [auth A], N [auth A], O [auth A], Q [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain T [auth B] SDF format, chain U [auth F] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth F]	K [auth A], L [auth A], M [auth A], T [auth B], U [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth F] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B]	I [auth A], J [auth A], R [auth B], S [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B]