6BXM | pdb_00006bxm

Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved SAM

• PDB DOI: https://doi.org/10.2210/pdb6BXM/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Candidatus Methanoperedens nitratireducens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-18 Released: 2018-04-11 
• Deposition Author(s): Fenwick, M.K., Torelli, A.T., Zhang, Y., Dong, M., Kathiresan, V., Carantoa, J.D., Dzikovski, B., Lancaster, K.M., Freed, J.H., Hoffman, B.M., Lin, H., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.

Dong, M., Kathiresan, V., Fenwick, M.K., Torelli, A.T., Zhang, Y., Caranto, J.D., Dzikovski, B., Sharma, A., Lancaster, K.M., Freed, J.H., Ealick, S.E., Hoffman, B.M., Lin, H.

(2018) Science 359: 1247-1250

• PubMed: 29590073 
• DOI: https://doi.org/10.1126/science.aao6595
• Primary Citation Related Structures: 
  6BXK, 6BXL, 6BXM, 6BXN, 6BXO


• PubMed Abstract: 
  

  Diphthamide biosynthesis involves a carbon-carbon bond-forming reaction catalyzed by a radical S-adenosylmethionine (SAM) enzyme that cleaves a carbon-sulfur (C-S) bond in SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. Using rapid freezing, we have captured an organometallic intermediate with an iron-carbon (Fe-C) bond between ACP and the enzyme's [4Fe-4S] cluster. In the presence of the substrate protein, elongation factor 2, this intermediate converts to an organic radical, formed by addition of the ACP radical to a histidine side chain. Crystal structures of archaeal diphthamide biosynthetic radical SAM enzymes reveal that the carbon of the SAM C-S bond being cleaved is positioned near the unique cluster Fe, able to react with the cluster. Our results explain how selective C-S bond cleavage is achieved in this radical SAM enzyme.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.
Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA. [e-mail] [e-mail] [e-mail].
Department of Chemistry, Northwestern University, Evanston, IL 60208, USA. [e-mail] [e-mail] [e-mail].
Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 74.42 kDa 
• Atom Count: 5,063 
• Modeled Residue Count: 632 
• Deposited Residue Count: 654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diphthamide biosynthesis enzyme Dph2	A, B	327	Candidatus Methanoperedens nitratireducens	Mutation(s): 0  Gene Names: ANME2D_01646 EC: 2.5.1.108
UniProt
Find proteins for A0A062UZ78 (Candidatus Methanoperedens nitratireducens) Explore A0A062UZ78  Go to UniProtKB:  A0A062UZ78

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	D [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SF4	C [auth A], E [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
MTA	G [auth B]	5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N
ABA	F [auth B]	ALPHA-AMINOBUTYRIC ACID C4 H9 N O2 QWCKQJZIFLGMSD-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.887	α = 90
b = 64.08	β = 90
c = 158.368	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-11 
Deposition Author(s): Fenwick, M.K., Torelli, A.T., Zhang, Y., Dong, M., Kathiresan, V., Carantoa, J.D., Dzikovski, B., Lancaster, K.M., Freed, J.H., Hoffman, B.M., Lin, H., Ealick, S.E.

Revision History  

• Version 1.0: 2018-04-11
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection