2OX5

The SoxYZ complex of Paracoccus pantotrophus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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: https://doi.org/10.1074/jbc.M701602200
  • Primary Citation of Related Structures:  
    2OX5, 2OXG, 2OXH

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SoxZ proteinA [auth Z],
C [auth A],
E [auth C],
G [auth E]
108Paracoccus denitrificansMutation(s): 0 
Gene Names: soxZ
UniProt
Find proteins for Q9LCU8 (Paracoccus denitrificans)
Explore Q9LCU8 
Go to UniProtKB:  Q9LCU8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LCU8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SoxY proteinB [auth Y],
D [auth B],
F [auth D],
H [auth F]
115Paracoccus denitrificansMutation(s): 0 
Gene Names: soxY
UniProt
Find proteins for Q9LCU9 (Paracoccus denitrificans)
Explore Q9LCU9 
Go to UniProtKB:  Q9LCU9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LCU9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth Y],
M [auth A],
R [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
T [auth F]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth Z]
J [auth Z]
L [auth A]
N [auth B]
O [auth B]
I [auth Z],
J [auth Z],
L [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
S [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth Z],
C [auth A],
E [auth C],
G [auth E]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
CME
Query on CME
B [auth Y],
D [auth B],
F [auth D],
H [auth F]
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 206.605α = 90
b = 54.708β = 98.58
c = 77.884γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOSFLMdata reduction
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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