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112  structures 1295  species 0  interactions 1573  sequences 30  architectures

Family: TPP_enzyme_M_2 (PF16582)

Summary: Middle domain of thiamine pyrophosphate

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Middle domain of thiamine pyrophosphate Provide feedback

TPP_enzyme_M_2 is the middle domain of thiamine pyrophosphate in sequences not captured by PF00205. This enzyme is necessary for the first step of the biosynthesis of menaquinone, or vitamin K2, an important cofactor in electron transport in bacteria [1].

Literature references

  1. Dawson A, Fyfe PK, Hunter WN;, J Mol Biol. 2008;384:1353-1368.: Specificity and reactivity in menaquinone biosynthesis: the structure of Escherichia coli MenD (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase). PUBMED:18983854 EPMC:18983854


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR032264

This entry represents the middle domain of menaquinone biosynthesis protein MenD, an enzyme that belongs to the thiamine pyrophosphate (TPP) enzyme family, but is not captured by INTERPRO . This enzyme is necessary for the first step of the biosynthesis of menaquinone, or vitamin K2, an important cofactor in electron transport in bacteria [ PUBMED:18983854 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan FAD_DHS (CL0085), which has the following description:

The members of this family adopt a Rossmann fold, similar to CLAN:CL0063. However, the members of this family are distinguished in that the FAD/NAD cofactor is bound in the opposite direction. In this arrangement, the adenosine moiety is found bound at the second half of the fold. In addition, the conserved GxGxxG motif found in classical NADP binding Rossmann folds is absent. Finally, another distinguishing characteristic is the formation of an internal hydrogen bond in the FAD molecule [1].

The clan contains the following 10 members:

CO_dh DS DUF4917 ETF_alpha PNTB PPS_PS SIR2 SIR2_2 TPP_enzyme_M TPP_enzyme_M_2

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(18)
Full
(1573)
Representative proteomes UniProt
(8934)
RP15
(172)
RP35
(682)
RP55
(1545)
RP75
(2850)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(18)
Full
(1573)
Representative proteomes UniProt
(8934)
RP15
(172)
RP35
(682)
RP55
(1545)
RP75
(2850)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(18)
Full
(1573)
Representative proteomes UniProt
(8934)
RP15
(172)
RP35
(682)
RP55
(1545)
RP75
(2850)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: pdb_2jla
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 18
Number in full: 1573
Average length of the domain: 208.4 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 27.82 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 30.1 30.1
Trusted cut-off 30.1 30.1
Noise cut-off 30.0 30.0
Model length: 208
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the TPP_enzyme_M_2 domain has been found. There are 112 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0H3GVP4 View 3D Structure Click here
A0A1D6HBM9 View 3D Structure Click here
A0A368UI94 View 3D Structure Click here
A0KFN8 View 3D Structure Click here
A1BI74 View 3D Structure Click here
A1SBA6 View 3D Structure Click here
A1SRV2 View 3D Structure Click here
A1WW41 View 3D Structure Click here
A3N348 View 3D Structure Click here
A3QJ17 View 3D Structure Click here
A4SD60 View 3D Structure Click here
A5GT34 View 3D Structure Click here
A5UPB5 View 3D Structure Click here
A6TBV8 View 3D Structure Click here
A6VMF8 View 3D Structure Click here
A8ADW9 View 3D Structure Click here
A8FGK9 View 3D Structure Click here
A8H9P4 View 3D Structure Click here
A9MJB6 View 3D Structure Click here
A9WB45 View 3D Structure Click here
B0C1Y1 View 3D Structure Click here
B0JII8 View 3D Structure Click here
B0UT51 View 3D Structure Click here
B1KM97 View 3D Structure Click here
B1WZR3 View 3D Structure Click here
B3EG68 View 3D Structure Click here
B4EZ42 View 3D Structure Click here
B4S4J4 View 3D Structure Click here
B4SET5 View 3D Structure Click here
B7K0T5 View 3D Structure Click here
B7K8M6 View 3D Structure Click here
B7VHY7 View 3D Structure Click here
C5B7I2 View 3D Structure Click here
K7MP48 View 3D Structure Click here
P17109 View 3D Structure Click here
P23970 View 3D Structure Click here
P44612 View 3D Structure Click here
Q089C0 View 3D Structure Click here
Q0I9Z1 View 3D Structure Click here
Q10XD8 View 3D Structure Click here