3TDG | pdb_00003tdg

Structural and functional characterization of Helicobacter pylori DsbG

• PDB DOI: https://doi.org/10.2210/pdb3TDG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-11 Released: 2011-11-09 
• Deposition Author(s): Yoon, J.Y., Kim, J., Lee, S.J., Kim, H.S., Im, H.N., Yoon, H., Kim, K.H., Kim, S., Han, B.W., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Structural and functional characterization of Helicobacter pylori DsbG

Yoon, J.Y., Kim, J., Lee, S.J., Kim, H.S., Im, H.N., Yoon, H., Kim, K.H., Kim, S., Han, B.W., Suh, S.W.

(2011) FEBS Lett 585: 3862-3867

• PubMed: 22062156 
• DOI: https://doi.org/10.1016/j.febslet.2011.10.042
• Primary Citation Related Structures: 
  3TDG


• PubMed Abstract: 
  

  Dsb proteins play important roles in bacterial pathogenicity. To better understand the role of Dsb proteins in Helicobacter pylori, we have structurally and functionally characterized H. pylori DsbG (HP0231). The monomer consists of two domains connected by a helical linker. Two monomers associate to form a V-shaped dimer. The monomeric and dimeric structures of H. pylori DsbG show significant differences compared to Escherichia coli DsbG. Two polyethylene glycol molecules are bound in the cleft of the V-shaped dimer, suggesting a possible role as a chaperone. Furthermore, we show that H. pylori DsbG functions as a reductase against HP0518, a putative L,D-transpeptidase with a catalytic cysteine residue.

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Organizational Affiliation: 
• Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.99 kDa 
• Atom Count: 1,974 
• Modeled Residue Count: 232 
• Deposited Residue Count: 273 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	273	Helicobacter pylori	Mutation(s): 0  Gene Names: HP_0231
UniProt
Find proteins for O25017 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25017  Go to UniProtKB:  O25017

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	D [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.767	α = 90
b = 86.767	β = 90
c = 85.508	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-09 
Deposition Author(s): Yoon, J.Y., Kim, J., Lee, S.J., Kim, H.S., Im, H.N., Yoon, H., Kim, K.H., Kim, S., Han, B.W., Suh, S.W.

Revision History  

• Version 1.0: 2011-11-09
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations