1AOP

SULFITE REDUCTASE STRUCTURE AT 1.6 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Sulfite reductase structure at 1.6 A: evolution and catalysis for reduction of inorganic anions.

Crane, B.R.Siegel, L.M.Getzoff, E.D.

(1995) Science 270: 59-67

  • DOI: 10.1126/science.270.5233.59
  • Primary Citation of Related Structures:  
    1AOP

  • PubMed Abstract: 
  • Fundamental chemical transformations for biogeochemical cycling of sulfur and nitrogen are catalyzed by sulfite and nitrite reductases. The crystallographic structure of Escherichia coli sulfite reductase hemoprotein (SiRHP), which catalyzes the concerted six-electron reductions of sulfite to sulfide and nitrite to ammonia, was solved with multiwavelength anomalous diffraction (MAD) of the native siroheme and Fe4S4 cluster cofactors, multiple isomorphous replacement, and selenomethionine sequence markers ...

    Fundamental chemical transformations for biogeochemical cycling of sulfur and nitrogen are catalyzed by sulfite and nitrite reductases. The crystallographic structure of Escherichia coli sulfite reductase hemoprotein (SiRHP), which catalyzes the concerted six-electron reductions of sulfite to sulfide and nitrite to ammonia, was solved with multiwavelength anomalous diffraction (MAD) of the native siroheme and Fe4S4 cluster cofactors, multiple isomorphous replacement, and selenomethionine sequence markers. Twofold symmetry within the 64-kilodalton polypeptide generates a distinctive three-domain alpha/beta fold that controls cofactor assembly and reactivity. Homology regions conserved between the symmetry-related halves of SiRHP and among other sulfite and nitrite reductases revealed key residues for stability and function, and identified a sulfite or nitrite reductase repeat (SNiRR) common to a redox-enzyme superfamily. The saddle-shaped siroheme shares a cysteine thiolate ligand with the Fe4S4 cluster and ligates an unexpected phosphate anion. In the substrate complex, sulfite displaces phosphate and binds to siroheme iron through sulfur. An extensive hydrogen-bonding network of positive side chains, water molecules, and siroheme carboxylates activates S-O bonds for reductive cleavage.


    Related Citations: 
    • Structures of the Siroheme-and Fe4S4-Containing Active Center of Sulfite Reductase in Different States of Oxidation: Heme Activation Via Reduction-Gated Exogenous Ligand Exchange
      Crane, B.R., Siegel, L.M., Getzoff, E.D.
      (1997) Biochemistry 36: 12101
    • Multiwavelength Anomalous Diffraction of Sulfite Reductase Hemoprotein: Making the Most of MAD Data
      Crane, B.R., Bellamy, H., Getzoff, E.D.
      (1997) Acta Crystallogr D Biol Crystallogr 53: 8
    • Determining Phases and Anomalous-Scattering Models from the Multiwavelength Anomalous Diffraction of Native Protein Metal Clusters. Improved MAD Phase Error Estimates and Anomalous-Scatterer Positions
      Crane, B.R., Getzoff, E.D.
      (1997) Acta Crystallogr D Biol Crystallogr 53: 23
    • Characterization of the Cysjih Regions of Salmonella Typhimurium and Escherichia Coli B. DNA Sequences of Cysi and Cysh and a Model for the Siroheme-Fe4S4 Active Center of Sulfite Reductase Hemoprotein Based on Amino Acid Homology with Spinach Nitrite Reductase
      Ostrowski, J., Wu, J.Y., Rueger, D.C., Miller, B.E., Siegel, L.M., Kredich, N.M.
      (1989) J Biol Chem 264: 15726
    • The Heme and Fe4S4 Cluster in the Crystallographic Structure of Escherichia Coli Sulfite Reductase
      Mcree, D.E., Richardson, D.C., Richardson, J.S., Siegel, L.M.
      (1986) J Biol Chem 261: 10277

    Organizational Affiliation

    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SULFITE REDUCTASE HEMOPROTEINA497Escherichia coli BMutation(s): 0 
Gene Names: CYSIJ
EC: 1.8.1.2
UniProt
Find proteins for P17846 (Escherichia coli (strain K12))
Explore P17846 
Go to UniProtKB:  P17846
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRM (Subject of Investigation/LOI)
Query on SRM

Download Ideal Coordinates CCD File 
E [auth A]SIROHEME
C42 H42 Fe N4 O16
PGYXHNRRBJLFEV-NBUGCWMUSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
D [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.8α = 90
b = 77.4β = 90
c = 87.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
ROTAVATAdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-12-24
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other, Refinement description