1D2M | pdb_00001d2m

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

• PDB DOI: https://doi.org/10.2210/pdb1D2M/pdb

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


• 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: 1.90 Å
• R-Value Free: 
  0.253 (Depositor) 
• R-Value Work: 
  0.234 (Depositor) 
• R-Value Observed: 
  0.234 (Depositor) 

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

• PubMed: 10578047 
• DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a022566
• Primary Citation 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. 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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Organizational Affiliation: 
• Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 77.24 kDa 
• Atom Count: 4,859 
• Modeled Residue Count: 552 
• Deposited Residue Count: 665 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXCINUCLEASE ABC SUBUNIT B	A	665	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], D [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

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

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.04	α = 90
b = 135.04	β = 90
c = 106.756	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  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
• Version 1.6: 2024-02-07
  Changes: Data collection, Database references, Structure summary