!!

Powering down the Pfam website
On October 5th, we will start redirecting the traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will be available at legacy.pfam.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
3  structures 237  species 0  interactions 476  sequences 4  architectures

Family: Latexin (PF06907)

Summary: Latexin

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Latexin family". More...

Latexin family Edit Wikipedia article

Latexin
PDB 2bo9 EBI.jpg
human carboxypeptidase a4 in complex with human latexin.
Identifiers
SymbolLatexin
PfamPF06907
InterProIPR009684

In molecular biology, the latexin family is a family of proteins which family consists of several animal specific latexin and proteins related to latexin that belong to MEROPS proteinase inhibitor family I47, clan IH.[1]

Latexin, a protein possessing inhibitory activity against rat carboxypeptidase A1 (CPA1) and CPA2 (MEROPS peptidase family M14A), is expressed in a neuronal subset in the cerebral cortex and cells in other neural and non-neural tissues of rat.[2][3] OCX-32, the 32 kDa eggshell matrix protein, is present at high levels in the uterine fluid during the terminal phase of eggshell formation, and is localised predominantly in the outer eggshell. The timing of OCX-32 secretion into the uterine fluid suggests that it may play a role in the termination of mineral deposition.[4] OCX-32 protein possesses limited identity (32%) to two unrelated proteins: latexin and to a skin protein that is encoded by a retinoic acid receptor-responsive gene, TIG1. Tazarotene Induced Gene 1 (TIG1) is a putative transmembrane protein with a small N-terminal intracellular region, a single membrane-spanning hydrophobic region, and a large C-terminal extracellular region containing a glycosylation signal. TIG1 is up-regulated by retinoic acid receptor but not by retinoid X receptor-specific synthetic retinoids.[5] TIG1 may be a tumour suppressor gene whose diminished expression is involved in the malignant progression of prostate cancer.[6]

External links

References

  1. ^ Rawlings ND, Tolle DP, Barrett AJ (2004). "Evolutionary families of peptidase inhibitors". Biochem. J. 378 (Pt 3): 705–16. doi:10.1042/BJ20031825. PMC 1224039. PMID 14705960. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ Uratani Y, Takiguchi-Hayashi K, Miyasaka N, Sato M, Jin M, Arimatsu Y (2000). "Latexin, a carboxypeptidase A inhibitor, is expressed in rat peritoneal mast cells and is associated with granular structures distinct from secretory granules and lysosomes". Biochem. J. 346 Pt 3: 817–26. PMC 1220918. PMID 10698712. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  3. ^ Liu Q, Yu L, Gao J, Fu Q, Zhang J, Zhang P, Chen J, Zhao S (2000). "Cloning, tissue expression pattern and genomic organization of latexin, a human homologue of rat carboxypeptidase A inhibitor". Mol. Biol. Rep. 27 (4): 241–6. PMID 11455960.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ Hincke MT, Gautron J, Mann K, Panheleux M, McKee MD, Bain M, Solomon SE, Nys Y (2003). "Purification of ovocalyxin-32, a novel chicken eggshell matrix protein". Connect. Tissue Res. 44 Suppl 1: 16–9. PMID 12952168.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  5. ^ Nagpal S, Patel S, Asano AT, Johnson AT, Duvic M, Chandraratna RA (1996). "Tazarotene-induced gene 1 (TIG1), a novel retinoic acid receptor-responsive gene in skin". J. Invest. Dermatol. 106 (2): 269–74. PMID 8601727. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  6. ^ Jing C, El-Ghany MA, Beesley C, Foster CS, Rudland PS, Smith P, Ke Y (2002). "Tazarotene-induced gene 1 (TIG1) expression in prostate carcinomas and its relationship to tumorigenicity". J. Natl. Cancer Inst. 94 (7): 482–90. PMID 11929948. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR009684

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Latexin Provide feedback

This family consists of several animal specific latexin proteins. Latexin is a carboxypeptidase A inhibitor and is expressed in a cell type-specific manner in both central and peripheral nervous systems in the rat [1].

Literature references

  1. Liu Q, Yu L, Gao J, Fu Q, Zhang J, Zhang P, Chen J, Zhao S; , Mol Biol Rep 2000;27:241-246.: Cloning, tissue expression pattern and genomic organization of latexin, a human homologue of rat carboxypeptidase A inhibitor. PUBMED:11455960 EPMC:11455960


This tab holds annotation information from the InterPro database.

InterPro entry IPR009684

This family consists of several animal specific latexin and proteins related to latexin that belong to MEROPS proteinase inhibitor family I47, clan I- [ PUBMED:14705960 ].

Latexin, a protein possessing inhibitory activity against rat carboxypeptidase A1 (CPA1) and CPA2 (MEROPS peptidase family M14A), is expressed in a neuronal subset in the cerebral cortex and cells in other neural and non-neural tissues of rat [ PUBMED:10698712 , PUBMED:11455960 ]. OCX-32, the 32kDa eggshell matrix protein, is present at high levels in the uterine fluid during the terminal phase of eggshell formation, and is localised predominantly in the outer eggshell. The timing of OCX-32 secretion into the uterine fluid suggests that it may play a role in the termination of mineral deposition [ PUBMED:12952168 ]. OCX-32 protein possesses limited identity (32%) to two unrelated proteins: latexin and to a skin protein that is encoded by a retinoic acid receptor-responsive gene, TIG1. Tazarotene Induced Gene 1 (TIG1) is a putative 228 transmembrane protein with a small N-terminal intracellular region, a single membrane-spanning hydrophobic region, and a large C-terminal extracellular region containing a glycosylation signal. TIG1 is up-regulated by retinoic acid receptor but not by retinoid X receptor-specific synthetic retinoids [ PUBMED:8601727 ]. TIG1 may be a tumour suppressor gene whose diminished expression is involved in the malignant progression of prostate cancer [ PUBMED:11929948 ].

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan Cystatin (CL0121), which has the following description:

This superfamily includes cystatins and cathelicidins [1]. The cystatin superfamily comprises cysteine protease inhibitors that play key regulatory roles in protein degradation processes. The progenitor of this superfamily was most probably intracellular and lacked a signal peptide and disulfide bridges, much like the extant Giardia cystatin. A primordial gene duplication produced two ancestral eukaryotic lineages, cystatins and stefins. Stefins - included in Pfam:PF00031 - remain encoded by a single or a small number of genes throughout the eukaryotes, whereas the cystatins have undergone a more complex and dynamic evolution through numerous gene and domain duplications [2].

The clan contains the following 13 members:

Cathelicidins Cystatin DUF3889 DUF5590 FTP Latexin Monellin PP1 Spp-24 SQAPI Staphopain_pro YebF YPEB

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
(16)
Full
(476)
Representative proteomes UniProt
(1049)
RP15
(34)
RP35
(129)
RP55
(362)
RP75
(500)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(16)
Full
(476)
Representative proteomes UniProt
(1049)
RP15
(34)
RP35
(129)
RP55
(362)
RP75
(500)
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
(16)
Full
(476)
Representative proteomes UniProt
(1049)
RP15
(34)
RP35
(129)
RP55
(362)
RP75
(500)
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_14203 (release 10.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Moxon SJ
Number in seed: 16
Number in full: 476
Average length of the domain: 187.9 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 81.91 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 26.3 25.1
Noise cut-off 21.0 20.7
Model length: 217
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 Latexin domain has been found. There are 3 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.

Loading structure mapping...

AlphaFold Structure Predictions