1C4O | pdb_00001c4o

CRYSTAL STRUCTURE OF THE DNA NUCLEOTIDE EXCISION REPAIR ENZYME UVRB FROM THERMUS THERMOPHILUS

• PDB DOI: https://doi.org/10.2210/pdb1C4O/pdb

• Classification: REPLICATION
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1999-09-14 Released: 2000-07-26 
• Deposition Author(s): Machius, M., Henry, L., Palnitkar, M., Deisenhofer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.266 (Depositor) 
• R-Value Work: 
  0.252 (Depositor) 
• R-Value Observed: 
  0.252 (Depositor) 

Literature

Crystal structure of the DNA nucleotide excision repair enzyme UvrB from Thermus thermophilus.

Machius, M., Henry, L., Palnitkar, M., Deisenhofer, J.

(1999) Proc Natl Acad Sci U S A 96: 11717-11722

• PubMed: 10518516 
• DOI: https://doi.org/10.1073/pnas.96.21.11717
• Primary Citation Related Structures: 
  1C4O


• PubMed Abstract: 
  

  Nucleotide excision repair (NER) is the most important DNA-repair mechanism in living organisms. In prokaryotes, three enzymes forming the UvrABC system initiate NER of a variety of structurally different DNA lesions. UvrB, the central component of this system, is responsible for the ultimate DNA damage recognition and participates in the incision of the damaged DNA strand. The crystal structure of Thermus thermophilus UvrB reveals a core that is structurally similar to core regions found in helicases, where they constitute molecular motors. Additional domains implicated in binding to DNA and various components of the NER system are attached to this central core. The architecture and distribution of DNA binding sites suggest a possible model for the DNA damage recognition process.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75235-9050, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 77.1 kDa 
• Atom Count: 4,453 
• Modeled Residue Count: 504 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA NUCLEOTIDE EXCISION REPAIR ENZYME UVRB	A	664	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q56243 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q56243  Go to UniProtKB:  Q56243

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	B [auth A], C [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.266 (Depositor) 
• R-Value Work:  0.252 (Depositor) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.74	α = 90
b = 134.74	β = 90
c = 106.7	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-07-26 
Deposition Author(s): Machius, M., Henry, L., Palnitkar, M., Deisenhofer, J.

Revision History  

• Version 1.0: 2000-07-26
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Advisory, Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-12-27
  Changes: Advisory, Data collection, Database references, Structure summary