4FYC | pdb_00004fyc

Structural and functional characterizations of a thioredoxin-fold protein from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 
    0.238 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural and functional characterization of HP0377, a thioredoxin-fold protein from Helicobacter pylori

Yoon, J.Y.Kim, J.An, D.R.Lee, S.J.Kim, H.S.Im, H.N.Yoon, H.J.Kim, J.Y.Kim, S.J.Han, B.W.Suh, S.W.

(2013) Acta Crystallogr D Biol Crystallogr 69: 735-746

  • DOI: https://doi.org/10.1107/S0907444913001236
  • Primary Citation Related Structures: 
    4FYB, 4FYC

  • PubMed Abstract: 

    Maturation of cytochrome c is carried out in the bacterial periplasm, where specialized thiol-disulfide oxidoreductases provide the correct reduction of oxidized apocytochrome c before covalent haem attachment. HP0377 from Helicobacter pylori is a thioredoxin-fold protein that has been implicated as a component of system II for cytochrome c assembly and shows limited sequence similarity to Escherichia coli DsbC, a disulfide-bond isomerase. To better understand the role of HP0377, its crystal structures have been determined in both reduced and partially oxidized states, which are highly similar to each other. Sedimentation-equilibrium experiments indicate that HP0377 is monomeric in solution. HP0377 adopts a thioredoxin fold but shows distinctive variations as in other thioredoxin-like bacterial periplasmic proteins. The active site of HP0377 closely resembles that of E. coli DsbC. A reductase assay suggests that HP0377 may play a role as a reductase in the biogenesis of holocytochrome c553 (HP1227). Binding experiments indicate that it can form a covalent complex with HP0518, a putative L,D-transpeptidase with a catalytic cysteine residue, via a disulfide bond. Furthermore, physicochemical properties of HP0377 and its R86A variant have been determined. These results suggest that HP0377 may perform multiple functions as a reductase in H. pylori.


  • Organizational Affiliation
    • Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 55.29 kDa 
  • Atom Count: 2,709 
  • Modeled Residue Count: 323 
  • Deposited Residue Count: 482 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thiol:disulfide interchange protein (DsbC)
A, B
241Helicobacter pylori 26695Mutation(s): 0 
Gene Names: HP_0377
UniProt
Find proteins for O25140 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25140 
Go to UniProtKB:  O25140
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25140
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
C [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free:  0.238 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.858α = 90
b = 43.953β = 112.29
c = 76.699γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description