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30  structures 348  species 0  interactions 378  sequences 1  architecture

Family: MetJ (PF01340)

Summary: Met Apo-repressor, MetJ

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Met Apo-repressor, MetJ Provide feedback

No Pfam abstract.

Literature references

  1. Rafferty JB, Somers WS, Saint-Girons I, Phillips SE; , Nature 1989;341:705-710.: Three-dimensional crystal structures of Escherichia coli met repressor with and without corepressor. PUBMED:2677753 EPMC:2677753

  2. Somers WS, Rafferty JB, Phillips K, Strathdee S, He YY, McNally T, Manfield I, Navratil O, Old IG, Saint-Girons I, et al; , Ann N Y Acad Sci 1994;726:105-117.: The Met repressor-operator complex: DNA recognition by beta-strands. PUBMED:8092669 EPMC:8092669

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002084

Binding of a specific DNA fragment and S-adenosyl methionine (SAM) co-repressor molecules to the Escherichia coli methionine repressor (MetJ) leads to a significant reduction in dynamic flexibility of the ternary complex, with considerable entropy-enthalpy compensation, not necessarily involving any overall conformational change [ PUBMED:8026581 ]. MetJ is a regulatory protein which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated.

MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer [ PUBMED:1943695 , PUBMED:10986458 , PUBMED:8092669 ].

The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognises sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs [ PUBMED:1406951 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 Met_repress (CL0057), which has the following description:

This superfamily contains many antitoxin families, all of which carry a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognising the major groove of operator DNA [1].

The clan contains the following 43 members:

Arc BrnA_antitoxin CcdA CopG_antitoxin DndE DUF1778 DUF1902 DUF2540 DUF2610 DUF6290 DUF6364 HicB HicB-like_2 HicB_lk_antitox MatP_C MetJ MobC MobC_2 Omega_Repress ParB_C ParD ParD_antitoxin ParD_like ParG Plasmid_stab_B PSK_trans_fac RelB RepB-RCR_reg Repressor_Mnt RHH_1 RHH_3 RHH_4 RHH_5 RHH_6 RHH_7 RHH_8 RHH_9 SeqA_N TraY VAPB_antitox VapB_antitoxin VirC2 VirD1


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

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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...


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.

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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: Sarah Teichmann
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A
Number in seed: 3
Number in full: 378
Average length of the domain: 95.90 aa
Average identity of full alignment: 77 %
Average coverage of the sequence by the domain: 88.04 %

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 25.0 25.0
Trusted cut-off 30.0 33.0
Noise cut-off 24.0 21.5
Model length: 97
Family (HMM) version: 22
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


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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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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 MetJ domain has been found. There are 30 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
P0A8U6 View 3D Structure Click here