2OXH

The SOXYZ Complex of Paracoccus Pantotrophus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The SoxYZ Complex Carries Sulfur Cycle Intermediates on a Peptide Swinging Arm.

Sauve, V.Bruno, S.Berks, B.C.Hemmings, A.M.

(2007) J.Biol.Chem. 282: 23194-23204

  • DOI: 10.1074/jbc.M701602200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The bacterial Sox (sulfur oxidizing) system allows the utilization of inorganic sulfur compounds in energy metabolism. Central to this process is the SoxYZ complex that carries the pathway intermediates on a cysteine residue near the C terminus of So ...

    The bacterial Sox (sulfur oxidizing) system allows the utilization of inorganic sulfur compounds in energy metabolism. Central to this process is the SoxYZ complex that carries the pathway intermediates on a cysteine residue near the C terminus of SoxY. Crystal structures have been determined for Paracoccus pantotrophus SoxYZ with the carrier cysteine in the underivatized state, conjugated to the polysulfide mimic beta-mercaptoethanol, and as the sulfonate adduct pathway intermediate. The carrier cysteine is located on a peptide swinging arm and is bracketed on either side by diglycine dipeptides acting as molecular universal joints. This structure provides a novel solution to the requirement that the cysteine-bound intermediates be able to access and orient themselves within the active sites of multiple partner enzymes. Adjacent to the swinging arm there is a conserved, deep, apolar pocket into which the beta-mercaptoethanol adduct extends. This pocket would be well suited to a role in protecting labile pathway intermediates from adventitious reactions.


    Organizational Affiliation

    Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SoxZ protein
Z, A, C, E
107Paracoccus denitrificansMutation(s): 0 
Gene Names: soxZ
Find proteins for Q9LCU8 (Paracoccus denitrificans)
Go to UniProtKB:  Q9LCU8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SoxY protein
Y, B, D, F
124Paracoccus denitrificansMutation(s): 0 
Gene Names: soxY
Find proteins for Q9LCU9 (Paracoccus denitrificans)
Go to UniProtKB:  Q9LCU9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, D, Y
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSU
Query on CSU
B, D, F, Y
L-PEPTIDE LINKINGC3 H7 N O5 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.194 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 40.220α = 103.13
b = 54.490β = 95.21
c = 104.872γ = 90.01
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
REFMACrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance