6P5Z

Cobalt-sirohydrochlorin-bound S. typhimurium siroheme synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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): 0 
Gene Names: cobAcysGC2253_19735CET98_25025D7F20_23535D7H43_21790DJ388_17225NCTC13348_03825
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
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F0X (Subject of Investigation/LOI)
Query on F0X

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
cobalt-sirohydrochlorin
C42 H44 Co N4 O16
RDAZHPPNZOKNBE-QIISWYHFSA-L
SAH
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.601α = 90
b = 100.446β = 90
c = 146.4γ = 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


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

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2021-12-29
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Refinement description