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109  structures 1440  species 0  interactions 6023  sequences 115  architectures

Family: MMS1_N (PF10433)

Summary: Mono-functional DNA-alkylating methyl methanesulfonate N-term

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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.

Mono-functional DNA-alkylating methyl methanesulfonate N-term Provide feedback

MMS1 is a protein that protects against replication-dependent DNA damage in Saccharomyces cerevisiae [1]. MMS1 belongs to the DDB1 family of cullin 4 adaptors and the two proteins are homologous. MMS1 bridges the interaction of MMS22 and Crt10 with Cul8/Rtt101 [2]. Cul8/Rtt101 is a cullin protein involved in the regulation of DNA replication subsequent to DNA damage. The N-terminal region of MMS1 and the C-terminal of MMS22 are required for the the MMS1-MMS22 interaction [3]. The human HIV-1 virion-associated protein Vpr assembles with DDB1 through interaction with DCAF1 (chromatin assembly factor) to form an E3 ubiquitin ligase that targets cellular substrates for proteasome-mediated degradation and subsequent G2 arrest [4].

Literature references

  1. Hryciw T, Tang M, Fontanie T, Xiao W; , Mol Genet Genomics. 2002;266:848-857.: MMS1 protects against replication-dependent DNA damage in Saccharomyces cerevisiae. PUBMED:11810260 EPMC:11810260

  2. Zaidi IW, Rabut G, Poveda A, Scheel H, Malmstrom J, Ulrich H, Hofmann K, Pasero P, Peter M, Luke B;, EMBO Rep. 2008;9:1034-1040.: Rtt101 and Mms1 in budding yeast form a CUL4(DDB1)-like ubiquitin ligase that promotes replication through damaged DNA. PUBMED:18704118 EPMC:18704118

  3. Mimura S, Yamaguchi T, Ishii S, Noro E, Katsura T, Obuse C, Kamura T;, J Biol Chem. 2010; [Epub ahead of print]: Cul8/Rtt101 forms a variety of protein complexes that regulate DNA damage response and transcriptional silencing. PUBMED:20139071 EPMC:20139071

  4. Tan L, Ehrlich E, Yu XF;, J Virol. 2007;81:10822-10830.: DDB1 and Cul4A are required for human immunodeficiency virus type 1 Vpr-induced G2 arrest. PUBMED:17626091 EPMC:17626091


This tab holds annotation information from the InterPro database.

InterPro entry IPR018846

This family includes a region that lies towards the N terminus of the cleavage and polyadenylation specificity factor (CPSF) A (160kDa) subunit. CPSF is involved in mRNA polyadenylation and binds the AAUAAA conserved sequence in pre-mRNA. CPSF has also been found to be necessary for splicing of single-intron pre-mRNAs [ PUBMED:11421366 ]. The function of the aligned region is unknown but may be involved in RNA/DNA binding.

Domain organisation

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

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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...

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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
(92)
Full
(6023)
Representative proteomes UniProt
(10251)
RP15
(1162)
RP35
(2856)
RP55
(4702)
RP75
(6309)
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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
(92)
Full
(6023)
Representative proteomes UniProt
(10251)
RP15
(1162)
RP35
(2856)
RP55
(4702)
RP75
(6309)
Alignment:
Format:
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Sequence:
Gaps:
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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
(92)
Full
(6023)
Representative proteomes UniProt
(10251)
RP15
(1162)
RP35
(2856)
RP55
(4702)
RP75
(6309)
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: Pfam-B_64607 (release 22.0)
Previous IDs: MMS1;
Type: Domain
Sequence Ontology: SO:0000417
Author: Mistry J , Wood V
Number in seed: 92
Number in full: 6023
Average length of the domain: 478.50 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 41.67 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.9 28.9
Trusted cut-off 29.1 28.9
Noise cut-off 28.8 28.8
Model length: 491
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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 MMS1_N domain has been found. There are 109 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
A0A0G2KCW6 View 3D Structure Click here
A0A0P0VEN2 View 3D Structure Click here
A0A0R0F241 View 3D Structure Click here
A0A0R0HF88 View 3D Structure Click here
A0A0R4IC37 View 3D Structure Click here
A0A1D6EE88 View 3D Structure Click here
A0A1D6FLI0 View 3D Structure Click here
A0A1D6GZZ1 View 3D Structure Click here
A0A1D6HVM7 View 3D Structure Click here
A0A1D6ME60 View 3D Structure Click here
A0A1D8PFJ5 View 3D Structure Click here
A0A368UI54 View 3D Structure Click here
A4HSL1 View 3D Structure Click here
A4I7V5 View 3D Structure Click here
B0M0P5 View 3D Structure Click here
B5DEL2 View 3D Structure Click here
E9PT66 View 3D Structure Click here
I1JQE1 View 3D Structure Click here
I1L3K1 View 3D Structure Click here
I1LFD7 View 3D Structure Click here
I1MQ84 View 3D Structure Click here
I1NJ61 View 3D Structure Click here
K7LU36 View 3D Structure Click here
O13807 View 3D Structure Click here
O44985 View 3D Structure Click here
O49552 View 3D Structure Click here
O74733 View 3D Structure Click here
P0DKL4 View 3D Structure Click here
P0DKL6 View 3D Structure Click here
Q04693 View 3D Structure Click here
Q0D7W8 View 3D Structure Click here
Q10141 View 3D Structure Click here
Q10426 View 3D Structure Click here
Q10570 View 3D Structure Click here
Q15393 View 3D Structure Click here
Q16531 View 3D Structure Click here
Q1LVE8 View 3D Structure Click here
Q21554 View 3D Structure Click here
Q3U1J4 View 3D Structure Click here
Q4D3X4 View 3D Structure Click here
Q4DNK0 View 3D Structure Click here
Q4DQ92 View 3D Structure Click here
Q4DQ92 View 3D Structure Click here
Q4DX64 View 3D Structure Click here
Q4DZW6 View 3D Structure Click here
Q4DZW6 View 3D Structure Click here
Q54SA7 View 3D Structure Click here
Q54TS6 View 3D Structure Click here
Q55BV8 View 3D Structure Click here
Q5A7S5 View 3D Structure Click here
Q6L4S0 View 3D Structure Click here
Q7XWP1 View 3D Structure Click here
Q84R20 View 3D Structure Click here
Q8I574 View 3D Structure Click here
Q921M3 View 3D Structure Click here
Q9EPU4 View 3D Structure Click here
Q9ESW0 View 3D Structure Click here
Q9FGR0 View 3D Structure Click here
Q9M0V3 View 3D Structure Click here
Q9N4C2 View 3D Structure Click here
Q9UTT2 View 3D Structure Click here
Q9V726 View 3D Structure Click here
Q9W0M7 View 3D Structure Click here
Q9XYZ5 View 3D Structure Click here