Summary: Metallopeptidase family M24
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Metallopeptidase family M24 Provide feedback
This family contains metallopeptidases. It also contains non-peptidase homologues such as the N terminal domain of Spt16 which is a histone H3-H4 binding module [3].
Literature references
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Roderick SL, Matthews BW , Biochemistry 1993;32:3907-3912.: Structure of the cobalt-dependent methionine aminopeptidase from Escherichia coli: a new type of proteolytic enzyme. PUBMED:8471602 EPMC:8471602
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Rawlings ND, Barrett AJ; , Meth Enzymol 1995;248:183-228.: Evolutionary families of metallopeptidases. PUBMED:7674922 EPMC:7674922
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Stuwe T, Hothorn M, Lejeune E, Rybin V, Bortfeld M, Scheffzek K, Ladurner AG; , Proc Natl Acad Sci U S A. 2008;105:8884-8889.: The FACT Spt16 "peptidase" domain is a histone H3-H4 binding module. PUBMED:18579787 EPMC:18579787
External database links
HOMSTRAD: | Peptidase_M24 |
MEROPS: | M24 |
PROSITE: | PDOC00417 PDOC00575 |
SCOP: | 1mat |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000994
This entry contains proteins that belong to MEROPS peptidase family M24 (clan MG), which share a common structural-fold, the "pita-bread" fold. The fold contains both alpha helices and an anti-parallel beta sheet within two structurally similar domains that are thought to be derived from an ancient gene duplication. The active site, where conserved, is located between the two domains. The fold is common to methionine aminopeptidase (EC), aminopeptidase P (EC), prolidase (EC), agropine synthase and creatinase (EC). Though many of these peptidases require a divalent cation, creatinase is not a metal-dependent enzyme [PUBMED:8146141, PUBMED:12136144, PUBMED:8471602].
The entry also contains proteins that have lost catalytic activity, for example Spt16, which is a component of the FACT complex. The crystal structure of the N-terminal domain of Spt16, determined to 2.1A, reveals an aminopeptidase P fold whose enzymatic activity has been lost. This fold binds directly to histones H3-H4 through a interaction with their globular core domains, as well as with their N-terminal tails [PUBMED:18579787].
The FACT complex is a stable heterodimer in Saccharomyces cerevisiae (Baker's yeast) comprising Spt16p (SWISSPROT, INTERPRO) and Pob3p (SWISSPROT, INTERPRO). The complex plays a role in transcription initiation and promotes binding of TATA-binding protein (TBP) to a TATA box in chromatin [PUBMED:15987999]; it also facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilising and then reassembling nucleosome structure [PUBMED:12524332, PUBMED:12934006, PUBMED:18579787].
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (405) |
Full (42074) |
Representative proteomes | UniProt (164676) |
NCBI (212644) |
Meta (9639) |
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RP15 (5390) |
RP35 (19004) |
RP55 (38598) |
RP75 (64968) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (405) |
Full (42074) |
Representative proteomes | UniProt (164676) |
NCBI (212644) |
Meta (9639) |
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RP15 (5390) |
RP35 (19004) |
RP55 (38598) |
RP75 (64968) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | SCOP |
Previous IDs: | pep_M24; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 405 |
Number in full: | 42074 |
Average length of the domain: | 226.20 aa |
Average identity of full alignment: | 22 % |
Average coverage of the sequence by the domain: | 54.61 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 209 | ||||||||||||
Family (HMM) version: | 25 | ||||||||||||
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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Interactions
There are 13 interactions for this family. More...
Creatinase_N FACT-Spt16_Nlob Creatinase_N Ribosomal_L36e AMP_N FACT-Spt16_Nlob Ribosomal_L21e Ribosomal_L18A Ribosomal_L30_N AMP_N Ribosomal_L30 Ribosomal_L16 Peptidase_M24Structures
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 Peptidase_M24 domain has been found. There are 397 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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