4G38

Mutational analysis of sulfite reductase hemoprotein reveals the mechanism for coordinated electron and proton transfer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mutational analysis of sulfite reductase hemoprotein reveals the mechanism for coordinated electron and proton transfer.

Smith, K.W.Stroupe, M.E.

(2012) Biochemistry 51: 9857-9868

  • DOI: 10.1021/bi300947a
  • Primary Citation of Related Structures:  4G39, 4HTR

  • PubMed Abstract: 
  • Sulfite reductase catalyzes the six-electron reduction of sulfite to sulfide. The active site, found in the hemoprotein subunit (SiRHP), sits on the distal face of a negatively charged porphyrinoid called siroheme whose central iron atom is coupled t ...

    Sulfite reductase catalyzes the six-electron reduction of sulfite to sulfide. The active site, found in the hemoprotein subunit (SiRHP), sits on the distal face of a negatively charged porphyrinoid called siroheme whose central iron atom is coupled to a proximal Fe(4)S(4) cluster. Four positively charged amino acids are positioned around the active site cavity. Together, these two arginines (R83 and R153) and two lysines (K215 and K217) mitigate the negative charge on the siroheme macrocycle. They also serve as a cage around the distally bound anion that tightens when substrate binds and an active site loop clamps down. Structures of native SiRHP point to these amino acids as being important, but their specific roles are ill-defined. Here, we have altered those four active site amino acids and one amino acid on the flexible loop (N149) to probe their roles in SiRHP activity. None of these positively charged residues is required for electron transfer, but only R83S and N149W variants can produce a fully reduced product. By measuring the electrons used per unit of reduced sulfur released, we show that K215, R153, and K217 are responsible for intermediate and late proton transfers, whereas N149 and R153 play a role in the structure of the flexible loop that controls anion binding and release. R83 is primarily responsible for siroheme binding. Together, the activities and structures of these variants reveal specific roles for each in anion binding and in coupled proton transfer that facilitates electron transfer.


    Organizational Affiliation

    Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sulfite reductase [NADPH] hemoprotein beta-component
A
570Escherichia coli (strain K12)Gene Names: cysI
EC: 1.8.1.2
Find proteins for P17846 (Escherichia coli (strain K12))
Go to UniProtKB:  P17846
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
SRM
Query on SRM

Download SDF File 
Download CCD File 
A
SIROHEME
C42 H42 Fe N4 O16
PGYXHNRRBJLFEV-NBUGCWMUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.140 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.327α = 90.00
b = 76.171β = 90.00
c = 81.463γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing
PDB_EXTRACTdata extraction
HKL-2000data collection
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-03-06
    Type: Database references