4PW3

Crystal structure of the sulfite dehydrogenase SorT from Sinorhizobium meliloti


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of interprotein electron transfer in bacterial sulfite oxidation.

McGrath, A.P.Laming, E.L.Casas Garcia, G.P.Kvansakul, M.Guss, J.M.Trewhella, J.Calmes, B.Bernhardt, P.V.Hanson, G.R.Kappler, U.Maher, M.J.

(2015) Elife 4: e09066-e09066

  • DOI: 10.7554/eLife.09066
  • Primary Citation of Related Structures:  
    4PW3, 4PW9, 4PWA

  • PubMed Abstract: 
  • Interprotein electron transfer underpins the essential processes of life and relies on the formation of specific, yet transient protein-protein interactions. In biological systems, the detoxification of sulfite is catalyzed by the sulfite-oxidizing enzymes (SOEs), which interact with an electron acceptor for catalytic turnover ...

    Interprotein electron transfer underpins the essential processes of life and relies on the formation of specific, yet transient protein-protein interactions. In biological systems, the detoxification of sulfite is catalyzed by the sulfite-oxidizing enzymes (SOEs), which interact with an electron acceptor for catalytic turnover. Here, we report the structural and functional analyses of the SOE SorT from Sinorhizobium meliloti and its cognate electron acceptor SorU. Kinetic and thermodynamic analyses of the SorT/SorU interaction show the complex is dynamic in solution, and that the proteins interact with Kd = 13.5 ± 0.8 μM. The crystal structures of the oxidized SorT and SorU, both in isolation and in complex, reveal the interface to be remarkably electrostatic, with an unusually large number of direct hydrogen bonding interactions. The assembly of the complex is accompanied by an adjustment in the structure of SorU, and conformational sampling provides a mechanism for dissociation of the SorT/SorU assembly.


    Organizational Affiliation

    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative sulfite oxidaseA, B, C, D369Sinorhizobium meliloti 1021Mutation(s): 0 
Gene Names: R02832SMc04049
EC: 1.8.3.1
Find proteins for Q92M24 (Rhizobium meliloti (strain 1021))
Explore Q92M24 
Go to UniProtKB:  Q92M24
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MSS
Query on MSS

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], H [auth C], J [auth D](MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM
C10 H12 Mo N5 O7 P S2
BDXDYZBRBRKVRM-MRZGRPIRSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth B], I [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.064α = 90
b = 92.225β = 89.74
c = 109.433γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2016-02-17
    Changes: Database references
  • Version 1.2: 2017-02-15
    Changes: Database references