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284  structures 8472  species 0  interactions 15277  sequences 115  architectures

Family: SHMT (PF00464)

Summary: Serine hydroxymethyltransferase

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Serine hydroxymethyltransferase Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR039429

Proteins containing this domain include serine hydroxymethyltransferase and fluorothreonine transaldolase.

Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate-dependent enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate to glycine and methylenetetrahydrofolate [ PUBMED:11063567 ]. This reaction generates single carbon units for purine, thymidine, and methionine biosynthesis. It belongs to the aspartate aminotransferase superfamily (fold type I) [ PUBMED:10828359 ]. The pyridoxal-P group is attached to a lysine residue around which the sequence is highly conserved in all forms of the enzyme [ PUBMED:8305478 ]. SHMT catalyses the transfer of a hydroxymethyl group from N5, N10- methylene tetrahydrofolate to glycine, resulting in the formation of serine and tetrahydrofolate. Both eukaryotic and prokaryotic SHMT enzymes form tight obligate homodimers and the mammalian enzyme forms a homotetramer [ PUBMED:10828359 , PUBMED:11877399 ].

Fluorothreonine transaldolase catalyzes the final step in 4-fluorothreonine biosynthesis. It mediates a L-threonine/fluoroaceldehyde to 4-fluoro-L-threonine/acetaldehyde crossover reaction. It shares protein sequence similarity with SHMT [ PUBMED:19101471 ].

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 PLP_aminotran (CL0061), which has the following description:

This superfamily contains a variety of PLP-dependent enzymes.

The clan contains the following 16 members:

Alliinase_C Aminotran_1_2 Aminotran_3 Aminotran_5 Asp_aminotransf Beta_elim_lyase ComK Cys_Met_Meta_PP DegT_DnrJ_EryC1 GDC-P Met_gamma_lyase OKR_DC_1 Pyridoxal_deC SelA SepSecS SHMT

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
(10)
Full
(15277)
Representative proteomes UniProt
(62097)
RP15
(2173)
RP35
(7238)
RP55
(14521)
RP75
(23867)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(10)
Full
(15277)
Representative proteomes UniProt
(62097)
RP15
(2173)
RP35
(7238)
RP55
(14521)
RP75
(23867)
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
(10)
Full
(15277)
Representative proteomes UniProt
(62097)
RP15
(2173)
RP35
(7238)
RP55
(14521)
RP75
(23867)
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: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 10
Number in full: 15277
Average length of the domain: 346.80 aa
Average identity of full alignment: 48 %
Average coverage of the sequence by the domain: 83.84 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.4 21.4
Trusted cut-off 21.4 21.4
Noise cut-off 21.3 21.3
Model length: 399
Family (HMM) version: 21
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 SHMT domain has been found. There are 284 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
A0A0P0XKK3 View 3D Structure Click here
A0A0P0Y248 View 3D Structure Click here
A0A0R0FP82 View 3D Structure Click here
A0A0R0FY73 View 3D Structure Click here
A0A0R0FY89 View 3D Structure Click here
A0A0R0GK79 View 3D Structure Click here
A0A0R0GX14 View 3D Structure Click here
A0A0R0H5U8 View 3D Structure Click here
A0A0R0H5U8 View 3D Structure Click here
A0A0R0IG25 View 3D Structure Click here
A0A0R0IP64 View 3D Structure Click here
A0A0R0IUS1 View 3D Structure Click here
A0A0R0IUS1 View 3D Structure Click here
A0A0R0KCM6 View 3D Structure Click here
A0A0R4J2Q8 View 3D Structure Click here
A0A0R4J3Y9 View 3D Structure Click here
A0A0R4J4J6 View 3D Structure Click here
A0A0R4J574 View 3D Structure Click here
A0A1D6E1X1 View 3D Structure Click here
A0A1D6F116 View 3D Structure Click here
A0A1D6F524 View 3D Structure Click here
A0A1D6FLE9 View 3D Structure Click here
A0A1D6G7R9 View 3D Structure Click here
A0A1D6KEN9 View 3D Structure Click here
A0A1D6LES7 View 3D Structure Click here
A0A1D6MQV8 View 3D Structure Click here
A0A1D8PRB3 View 3D Structure Click here
A4HW78 View 3D Structure Click here
A4I3W7 View 3D Structure Click here
A9LDD9 View 3D Structure Click here
B4F947 View 3D Structure Click here
C6ZJY6 View 3D Structure Click here
C6ZJY9 View 3D Structure Click here
C6ZJZ0 View 3D Structure Click here
I1L4U2 View 3D Structure Click here
K7KUF0 View 3D Structure Click here
K7TSD2 View 3D Structure Click here
O13426 View 3D Structure Click here
O13972 View 3D Structure Click here
O23254 View 3D Structure Click here
P0A825 View 3D Structure Click here
P34896 View 3D Structure Click here
P34897 View 3D Structure Click here
P37291 View 3D Structure Click here
P37292 View 3D Structure Click here
P50431 View 3D Structure Click here
P50432 View 3D Structure Click here
P9WGI7 View 3D Structure Click here
P9WGI9 View 3D Structure Click here
Q10104 View 3D Structure Click here
Q10D68 View 3D Structure Click here
Q2FWE5 View 3D Structure Click here
Q2QT32 View 3D Structure Click here
Q4D7D8 View 3D Structure Click here
Q4DSP9 View 3D Structure Click here
Q54EW1 View 3D Structure Click here
Q54Z26 View 3D Structure Click here
Q58992 View 3D Structure Click here
Q5U3Z7 View 3D Structure Click here
Q6NYR0 View 3D Structure Click here
Q6TXG7 View 3D Structure Click here
Q75HP7 View 3D Structure Click here
Q84WV0 View 3D Structure Click here
Q8I566 View 3D Structure Click here
Q8IKR8 View 3D Structure Click here
Q8RYY6 View 3D Structure Click here
Q94C74 View 3D Structure Click here
Q94JQ3 View 3D Structure Click here
Q9CZN7 View 3D Structure Click here
Q9LM59 View 3D Structure Click here
Q9SVM4 View 3D Structure Click here
Q9SZJ5 View 3D Structure Click here
Q9W457 View 3D Structure Click here