6PR0

P133H-S128A S. typhimurium siroheme synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

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This is version 1.1 of the entry. See complete history


Literature

Siroheme synthase orients substrates for dehydrogenase and chelatase activities in a common active site.

Pennington, J.M.Kemp, M.McGarry, L.Chen, Y.Stroupe, M.E.

(2020) Nat Commun 11: 864-864

  • DOI: https://doi.org/10.1038/s41467-020-14722-1
  • Primary Citation of Related Structures:  
    6P5X, 6P5Z, 6P7C, 6P7D, 6PQZ, 6PR0, 6PR1, 6PR2, 6PR3, 6PR4, 6ULU, 6VEB

  • PubMed Abstract: 

    Siroheme is the central cofactor in a conserved class of sulfite and nitrite reductases that catalyze the six-electron reduction of sulfite to sulfide and nitrite to ammonia. In Salmonella enterica serovar Typhimurium, siroheme is produced by a trifunctional enzyme, siroheme synthase (CysG). A bifunctional active site that is distinct from its methyltransferase activity catalyzes the final two steps, NAD + -dependent dehydrogenation and iron chelation. How this active site performs such different chemistries is unknown. Here, we report the structures of CysG bound to precorrin-2, the initial substrate; sirohydrochlorin, the dehydrogenation product/chelation substrate; and a cobalt-sirohydrochlorin product. We identified binding poses for all three tetrapyrroles and tested the roles of specific amino acids in both activities to give insights into how a bifunctional active site catalyzes two different chemistries and acts as an iron-specific chelatase in the final step of siroheme synthesis.


  • Organizational Affiliation

    Department of Biological Science and Institute of Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, FL, 32306, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Siroheme synthase
A, B
457Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 1 
Gene Names: 
EC: 2.1.1.107 (PDB Primary Data), 1.3.1.76 (PDB Primary Data), 4.99.1.4 (PDB Primary Data)
UniProt
Find proteins for P25924 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P25924 
Go to UniProtKB:  P25924
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25924
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.828α = 90
b = 99.882β = 90
c = 146.544γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description