1D2M

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.4 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.(Tokyo) 126: 986-990


  • 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 comprise ...

    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.,Sect.D 55: 704


    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
MoleculeChainsSequence LengthOrganismDetails
EXCINUCLEASE ABC SUBUNIT B
A
665Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: uvrB
Find proteins for Q56243 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q56243
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BOG
Query on BOG

Download SDF File 
Download CCD File 
A
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
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 = 135.040α = 90.00
b = 135.040β = 90.00
c = 106.756γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
MLPHAREphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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