Top Level Name

  ⌊ Superfamily (extended) Radical SAM 3-amino-3-carboxypropyl Radical Forming

Family known
Total 100% <100% Family unknown
Functional domains 2420 1024 180 1216
UniProtKB 2306 823 172 1311
GI 4318 1497 426 2395
Structures 2
Reactions 0
Functional domains of this superfamily were last updated on June 10, 2017
New functional domains were last added to this superfamily on March 23, 2015

Diphthamide, the target of diphtheria toxin, is a unique posttranslational modification on translation elongation factor 2 (EF2) in archaea and eukaryotes. The biosynthesis of diphthamide is proposed to involve three steps. The first step of which is the transfer of the 3-amino-3-carboxypropyl group from S-adenosyl-l-methionine (SAM) to the histidine residue of EF2, forming a C–C bond. This step requires four proteins Dph1-Dph4. Dph2 is is radical SAM-like protein which forms a homodimer in Pyrococcus horikoshii and a complex with Dph1 in yeast that is responsible for the first step. Dph3 has been demonstrated to act as the electron donor for the radical SAM FeS reduction in this system.

Uses SAM and a 4Fe-4S cluster to form a 3-amino-3-carboxypropyl radical intermediate. No obvious structural or sequence similarity to the main Radical SAM superfamily. The reference cited for this superfamily describes the function of the only defined family identified to date.

Zhang Y, Zhu X, Torelli AT, Lee M, Dzikovski B, Koralewski RM, Wang E, Freed J, Krebs C, Ealick SE, Lin H

Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme

▸ Abstract

Nature 2010;465(7300):891-896 | PubMed ID: 20559380

Dong M, Su X, Dzikovski B, Dando EE, Zhu X, Du J, Freed JH, Lin H

Dph3 is an electron donor for Dph1-Dph2 in the first step of eukaryotic diphthamide biosynthesis

▸ Abstract

J Am Chem Soc 2014;136(5):1754-1757 | PubMed ID: 24422557

Dong M, Horitani M, Dzikovski B, Pandelia ME, Krebs C, Freed JH, Hoffman BM, Lin H

Organometallic Complex Formed by an Unconventional Radical S-Adenosylmethionine Enzyme

▸ Abstract

J Am Chem Soc 2016;None(None):None-None | PubMed ID: 27465315

Previous genetic studies showed this step requires four proteins in eukaryotes, Dph1–Dph4. However, the exact molecular functions for the four proteins are unknown. Previous study showed that Pyrococcus horikoshii Dph2 (PhDph2), a novel iron-sulfur cluster-containing enzyme, forms a homodimer and is sufficient for the first step of diphthamide biosynthesis in vitro. Here we demonstrate by in vitro reconstitution that yeast Dph1 and Dph2 form a complex (Dph1-Dph2) that is equivalent to the homodimer of PhDph2 and is sufficient to catalyze the first step in vitro in the presence of dithionite as the reductant. We further demonstrate that yeast Dph3 (also known as KTI11), a CSL-type zinc finger protein, can bind iron and in the reduced state can serve as an electron donor to reduce the Fe-S cluster in Dph1-Dph2. Our study thus firmly establishes the functions for three of the proteins involved in eukaryotic diphthamide biosynthesis. For most radical SAM enzymes in bacteria, flavodoxins and flavodoxin reductases are believed to serve as electron donors for the Fe-S clusters. The finding that Dph3 is an electron donor for the Fe-S clusters in Dph1-Dph2 is thus interesting and opens up new avenues of research on electron transfer to Fe-S proteins in eukaryotic cells.


[4Fe-4S]+ Cluster (complex)

S-Adenosylmethionine (coenzyme)

Sequence Similarity Networks

Download a Sequence Similarity Network of this superfamily (XGMML format ).

Network downloads are XGMML files that are readable by program such as Cytoscape. In these networks, nodes represent proteins and edges represent pairwise similarities better than a given edge-score cutoff. The edge score is either a bit score for full networks or mean E values for a Repnet. Additionally, these networks contain several attributes with data from the SFLD.

Select any restriction to apply to your network.
Maximum number of edges:
250K 500K 750K ALL
edge-score cutoff

List of files included in the download. A detailed list of included node attributes, their definitions, and their uses [revised: 1/24/2014].

Although the download speed has improved please keep in mind that network files can be quite large. We are currently working on improving the network download and finding ways to make large networks manageable. Please see How to increase memory for Cytoscape.

Multiple Sequence Alignment

View the alignment of a representative set of sequences of this superfamily using

Multiple Sequence Alignment

Align one or multiple sequences to the alignment of a representative set of sequences of this superfamily.
Enter FASTA formatted sequence(s) : and view results using


Data Type All (#) Known (#) Unknown (#)
Full length FASTA (2420) (1204) (1216)
Complete annotation (.tsv) (2420) (1204) (1216)
Annotation suitable for Excel ® (.tsv) (2420) (1204) (1216)
Clear form

Some of these files can be quite large, please be patient during the download.

To identify your sequence later, please make sure to provide a header line starting with '>' for each sequence. Empty headers are allowed, but a header line is always required.
Cutoff Value
The least significant edge-score at which pairwise similarities are included in the network. A bit score for the full network, or a mean E value for the Repnet.
XGMML format
Open in Cytoscape via:
 →Network (multiple file types)
Download the annotation of all sequences as shown in the table below as a ͟Tab ͟Separated ͟Value (TSV) file. This file can be imported into a spreadsheet application.
Full length FASTA
Full length sequences in FASTA format.
Functional Domain FASTA
Sequences of the Functional Domain in FASTA format.
Complete annotation
Download complete annotation of sequences sets of this superfamily as a ͟Tab ͟Separated ͟Value (TSV) file. This file has all data but cell size can exceed the maximum supported by spreadsheet programs (such as Microsoft Excel ®).
Spreadsheet ready annotation
Annotation of sequences sets of this superfamily in a ͟Tab ͟Separated ͟Value (TSV) file. This file can be imported into a spreadsheet application. Cells which exceed the allowed spreadsheet maximum (32.5K) are preceded by the word "Truncated" and clipped short.
Total number of functional domains in this group.
Number of Functional Domains that have been manually or automatically been assigned to a family.
Number of Functional Domains that have not been assigned to a family.
Number of structures available from the PDB for members of this group.
Number of Functional Domains with 100% of Conserved Residues
Number of Functional Domains with less than 100% Conserved Residues
Depth of the multi-level Subgroup hierarchy.