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449  structures 8825  species 0  interactions 49758  sequences 400  architectures

Family: Peptidase_M24 (PF00557)

Summary: Metallopeptidase family M24

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.

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

  1. 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

  2. Rawlings ND, Barrett AJ; , Meth Enzymol 1995;248:183-228.: Evolutionary families of metallopeptidases. PUBMED:7674922 EPMC:7674922

  3. 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

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 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
(383)
Full
(49758)
Representative proteomes UniProt
(193797)
RP15
(6965)
RP35
(23126)
RP55
(46720)
RP75
(76591)
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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
(383)
Full
(49758)
Representative proteomes UniProt
(193797)
RP15
(6965)
RP35
(23126)
RP55
(46720)
RP75
(76591)
Alignment:
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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
(383)
Full
(49758)
Representative proteomes UniProt
(193797)
RP15
(6965)
RP35
(23126)
RP55
(46720)
RP75
(76591)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: SCOP
Previous IDs: pep_M24;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 383
Number in full: 49758
Average length of the domain: 225.70 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 54.17 %

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 23.0 23.0
Trusted cut-off 23.0 23.0
Noise cut-off 22.9 22.9
Model length: 209
Family (HMM) version: 26
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 Peptidase_M24 domain has been found. There are 449 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
A0A0G2KZA4 View 3D Structure Click here
A0A0P0XJS0 View 3D Structure Click here
A0A0P0YCB1 View 3D Structure Click here
A0A0R0F3E9 View 3D Structure Click here
A0A0R0LM01 View 3D Structure Click here
A0A0R4IUB7 View 3D Structure Click here
A0A0R4J3P8 View 3D Structure Click here
A0A144A2H0 View 3D Structure Click here
A0A1D6DZY8 View 3D Structure Click here
A0A1D6FRI4 View 3D Structure Click here
A0A1D6GYM8 View 3D Structure Click here
A0A1D6HVR1 View 3D Structure Click here
A0A1D6KDB2 View 3D Structure Click here
A0A1D6KR54 View 3D Structure Click here
A0A1D6KR57 View 3D Structure Click here
A0A1D6P529 View 3D Structure Click here
A0A1D6PU20 View 3D Structure Click here
A0A1D6PWL4 View 3D Structure Click here
A0A1D8PFY5 View 3D Structure Click here
A0A1D8PG26 View 3D Structure Click here
A0A1D8PMP9 View 3D Structure Click here
A0A1D8PR11 View 3D Structure Click here
A0A1D8PSI7 View 3D Structure Click here
A0A286Y8E9 View 3D Structure Click here
A4HRK6 View 3D Structure Click here
A4HVJ6 View 3D Structure Click here
A4HY76 View 3D Structure Click here
A4HZM5 View 3D Structure Click here
A4I439 View 3D Structure Click here
A4IBC7 View 3D Structure Click here
A4IDX0 View 3D Structure Click here
A5A4L9 View 3D Structure Click here
A5WVX8 View 3D Structure Click here
A8KBZ9 View 3D Structure Click here
B1AVD1 View 3D Structure Click here
B4FKE6 View 3D Structure Click here
B4FQH9 View 3D Structure Click here
B4FSK5 View 3D Structure Click here
B4G1F6 View 3D Structure Click here
B5DEQ3 View 3D Structure Click here
B6TBW4 View 3D Structure Click here
B7ZMP1 View 3D Structure Click here
C0P7J4 View 3D Structure Click here
C6TCX5 View 3D Structure Click here
C6TL11 View 3D Structure Click here
D3ZE72 View 3D Structure Click here
D4A4J0 View 3D Structure Click here
E9AGR8 View 3D Structure Click here
E9AHA3 View 3D Structure Click here
F4HZG9 View 3D Structure Click here
F4JQH3 View 3D Structure Click here
G3V670 View 3D Structure Click here
H1UBK1 View 3D Structure Click here
I1J6Q1 View 3D Structure Click here
I1J7C8 View 3D Structure Click here
I1J7T4 View 3D Structure Click here
I1J8Y0 View 3D Structure Click here
I1JDW6 View 3D Structure Click here
I1JLC4 View 3D Structure Click here
I1K635 View 3D Structure Click here
I1LB32 View 3D Structure Click here
I1LHN4 View 3D Structure Click here
I1LM70 View 3D Structure Click here
I1LM72 View 3D Structure Click here
I1NEY0 View 3D Structure Click here
I6YDN6 View 3D Structure Click here
K7KCI9 View 3D Structure Click here
K7L4P0 View 3D Structure Click here
K7L4P2 View 3D Structure Click here
K7MPW8 View 3D Structure Click here
K7MPW9 View 3D Structure Click here
K7MVR5 View 3D Structure Click here
O08663 View 3D Structure Click here
O43895 View 3D Structure Click here
O44750 View 3D Structure Click here
O44995 View 3D Structure Click here
O54975 View 3D Structure Click here
O59730 View 3D Structure Click here
O60085 View 3D Structure Click here
O60180 View 3D Structure Click here
O61710 View 3D Structure Click here
O82491 View 3D Structure Click here
O94267 View 3D Structure Click here
P0AE18 View 3D Structure Click here
P12955 View 3D Structure Click here
P15034 View 3D Structure Click here
P21165 View 3D Structure Click here
P32558 View 3D Structure Click here
P38062 View 3D Structure Click here
P38174 View 3D Structure Click here
P40051 View 3D Structure Click here
P43590 View 3D Structure Click here
P50579 View 3D Structure Click here
P50580 View 3D Structure Click here
P53582 View 3D Structure Click here
P76524 View 3D Structure Click here
P9WHS7 View 3D Structure Click here
P9WK19 View 3D Structure Click here
P9WK21 View 3D Structure Click here
Q01662 View 3D Structure Click here
Q03862 View 3D Structure Click here
Q07825 View 3D Structure Click here
Q09184 View 3D Structure Click here
Q09795 View 3D Structure Click here
Q0ISB4 View 3D Structure Click here
Q0ISB6 View 3D Structure Click here
Q0JA93 View 3D Structure Click here
Q0WUQ7 View 3D Structure Click here
Q10439 View 3D Structure Click here
Q11136 View 3D Structure Click here
Q1ZXG4 View 3D Structure Click here
Q2FX05 View 3D Structure Click here
Q2FXL9 View 3D Structure Click here
Q2FY40 View 3D Structure Click here
Q2QNJ1 View 3D Structure Click here
Q2QRX9 View 3D Structure Click here
Q337D3 View 3D Structure Click here
Q4CP43 View 3D Structure Click here
Q4CQY3 View 3D Structure Click here
Q4CSP6 View 3D Structure Click here
Q4D031 View 3D Structure Click here
Q4D257 View 3D Structure Click here
Q4DD17 View 3D Structure Click here
Q4DFX9 View 3D Structure Click here
Q4DGA5 View 3D Structure Click here
Q4DGT8 View 3D Structure Click here
Q4DHU1 View 3D Structure Click here
Q4DRC6 View 3D Structure Click here
Q4DS97 View 3D Structure Click here
Q4DYJ8 View 3D Structure Click here
Q4QRK0 View 3D Structure Click here
Q4VBS4 View 3D Structure Click here
Q54G06 View 3D Structure Click here
Q54S43 View 3D Structure Click here
Q54T46 View 3D Structure Click here
Q54VU7 View 3D Structure Click here
Q54WU3 View 3D Structure Click here
Q55C21 View 3D Structure Click here
Q55E60 View 3D Structure Click here
Q56Y85 View 3D Structure Click here
Q58216 View 3D Structure Click here
Q59LF9 View 3D Structure Click here
Q5A1D5 View 3D Structure Click here
Q5AEB4 View 3D Structure Click here
Q5AI37 View 3D Structure Click here
Q5I0D7 View 3D Structure Click here
Q5W6H1 View 3D Structure Click here
Q6AYD3 View 3D Structure Click here
Q6P1B1 View 3D Structure Click here
Q6PHD8 View 3D Structure Click here
Q6UB28 View 3D Structure Click here
Q6Z3V9 View 3D Structure Click here
Q6Z4B5 View 3D Structure Click here
Q6Z6H2 View 3D Structure Click here
Q6Z6H2 View 3D Structure Click here
Q6Z8B5 View 3D Structure Click here
Q6ZIY1 View 3D Structure Click here
Q6ZM25 View 3D Structure Click here
Q7TP85 View 3D Structure Click here
Q7X923 View 3D Structure Click here
Q8AW82 View 3D Structure Click here
Q8BP48 View 3D Structure Click here
Q8H6B1 View 3D Structure Click here
Q8I3J2 View 3D Structure Click here
Q8I3T4 View 3D Structure Click here
Q8IAP0 View 3D Structure Click here
Q8IAP0 View 3D Structure Click here
Q8IJP2 View 3D Structure Click here
Q8ILB8 View 3D Structure Click here
Q8ILI2 View 3D Structure Click here
Q8IPS7 View 3D Structure Click here
Q8IRG6 View 3D Structure Click here
Q8RY11 View 3D Structure Click here
Q920B9 View 3D Structure Click here
Q96327 View 3D Structure Click here
Q965Y1 View 3D Structure Click here
Q99MA2 View 3D Structure Click here
Q9CPW9 View 3D Structure Click here
Q9FV49 View 3D Structure Click here
Q9FV50 View 3D Structure Click here
Q9FV51 View 3D Structure Click here
Q9FV52 View 3D Structure Click here
Q9GUI6 View 3D Structure Click here
Q9N5B3 View 3D Structure Click here
Q9N5R9 View 3D Structure Click here
Q9NQH7 View 3D Structure Click here
Q9NQW7 View 3D Structure Click here
Q9SLN5 View 3D Structure Click here
Q9UQ80 View 3D Structure Click here
Q9UUD8 View 3D Structure Click here
Q9VC48 View 3D Structure Click here
Q9VG44 View 3D Structure Click here
Q9VG79 View 3D Structure Click here
Q9VJG0 View 3D Structure Click here
Q9VKV9 View 3D Structure Click here
Q9VL89 View 3D Structure Click here
Q9VRP2 View 3D Structure Click here
Q9W5W7 View 3D Structure Click here
Q9Y5B9 View 3D Structure Click here