6C3Y

Wild type structure of SiRHP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 

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This is version 1.2 of the entry. See complete history


Literature

The role of extended Fe4S4cluster ligands in mediating sulfite reductase hemoprotein activity.

Cepeda, M.R.McGarry, L.Pennington, J.M.Krzystek, J.Stroupe, M.E.

(2018) Biochim Biophys Acta 1866: 933-940

  • DOI: 10.1016/j.bbapap.2018.05.013
  • Primary Citation of Related Structures:  
    6C3M, 6C3X, 6C3Y, 6C3Z

  • PubMed Abstract: 
  • The siroheme-containing subunit from the multimeric hemoflavoprotein NADPH-dependent sulfite reductase (SiR/SiRHP) catalyzes the six electron-reduction of SO 3 2- to S 2- . Siroheme is an iron-containing isobacteriochlorin that is found in sulfite and homologous siroheme-containing nitrite reductases ...

    The siroheme-containing subunit from the multimeric hemoflavoprotein NADPH-dependent sulfite reductase (SiR/SiRHP) catalyzes the six electron-reduction of SO 3 2- to S 2- . Siroheme is an iron-containing isobacteriochlorin that is found in sulfite and homologous siroheme-containing nitrite reductases. Siroheme does not work alone but is covalently coupled to a Fe 4 S 4 cluster through one of the cluster's ligands. One long-standing hypothesis predicted from this observation is that the environment of one iron-containing cofactor influences the properties of the other. We tested this hypothesis by identifying three amino acids (F437, M444, and T477) that interact with the Fe 4 S 4 cluster and probing the effect of altering them to alanine on the function and structure of the resulting enzymes by use of activity assays, X-ray crystallographic analysis, and EPR spectroscopy. We showed that F437 and M444 gate access for electron transfer to the siroheme-cluster assembly and the direct hydrogen bond between T477 and one of the cluster sulfides is important for determining the geometry of the siroheme active site.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sulfite reductase [NADPH] hemoprotein beta-componentA570Escherichia coli K-12Mutation(s): 1 
Gene Names: cysIb2763JW2733
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: 1.54 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.823α = 90
b = 77.262β = 90
c = 87.614γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-01-11 
  • Released Date: 2018-06-13 
  • Deposition Author(s): Stroupe, M.E.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB1149763

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence