1D2M

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


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 126: 986-990

  • DOI: 10.1093/oxfordjournals.jbchem.a022566
  • Primary Citation of Related Structures:  
    1D2M

  • 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 ...

    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.

    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 D Biol Crystallogr 55: 704
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EXCINUCLEASE ABC SUBUNIT BA665Thermus thermophilus HB8Mutation(s): 0 
Gene Names: uvrB, TTHA1892
UniProt
Find proteins for Q56243 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q56243 
Go to UniProtKB:  Q56243
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56243
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.04α = 90
b = 135.04β = 90
c = 106.756γ = 120
Software Package:
Software NamePurpose
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Database references
  • Version 1.4: 2018-01-31
    Changes: Database references
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary