Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 77239.29 
• Atom Count: 4524 
• Residue Count: 665 
• Unique protein chains: 1

1D2M

UVRB PROTEIN OF THERMUS THERMOPHILUS HB8; A NUCLEOTIDE EXCISION REPAIR ENZYME

• DOI: 10.2210/pdb1D2M/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
• Expression System: Escherichia coli


• Deposited: 1999-09-25 Released: 2000-03-22 
• Deposition Author(s): Nakagawa, N., Sugahara, M., Masui, R., Kato, R., Fukuyama, K., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.253 
• R-Value Work: 0.234 

Literature

Crystal structure of Thermus thermophilus HB8 UvrB protein, a key enzyme of nucleotide excision repair.

Nakagawa, N., Sugahara, M., Masui, R., Kato, R., Fukuyama, K., Kuramitsu, S.

(1999) J.Biochem.(Tokyo) 126: 986-990

• PubMed: 10578047 


• PubMed Abstract: 
  

In the nucleotide excision repair system, UvrB plays a central role in damage recognition and DNA incision by interacting with UvrA and UvrC. We have determined the crystal structure of Thermus thermophilus HB8 UvrB at 1.9 A resolution. UvrB comprises four domains, two of which have an alpha/beta structure resembling the core domains of DNA and RNA helicases. Additionally, UvrB has an alpha-helical domain and a domain consisting of antiparallel beta-sheets (beta-domain). The sequence similarity suggests that the beta-domain interacts with UvrA. Based on the distribution of the conserved regions and the structure of the PcrA-DNA complex, a model for the UvrB-DNA complex is proposed.

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Related Citations: 

• Crystallization and Preliminary X-ray Diffraction Studies of a DNA Excision Repair Enzyme, UvrB, from Thermus thermophilus HB8
  Shibata, A.,Nakagawa, N.,Sugahara, M.,Masui, R.,Kato, R.,Kuramitsu, S.,Fukuyama, S.
  (1999) Acta Crystallogr.,Sect.D 55: 704




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Organizational Affiliation: 

Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
EXCINUCLEASE ABC SUBUNIT B	A	665	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: uvrB
Find proteins for Q56243 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q56243

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BOG	A	B-OCTYLGLUCOSIDE C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.253 
• R-Value Work: 0.234 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 135.040	α = 90.00
b = 135.040	β = 90.00
c = 106.756	γ = 120.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
DENZO	data reduction
MLPHARE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-09-25 
• Released Date: 2000-03-22 
• Deposition Author(s): Nakagawa, N., Sugahara, M., Masui, R., Kato, R., Fukuyama, K., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History 

• Version 1.0: 2000-03-22
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Source and taxonomy, Version format compliance
• Version 1.3: 2018-01-24
  Type: Database references
• Version 1.4: 2018-01-31
  Type: Database references