Summary: Secreted protein acidic and rich in cysteine Ca binding region
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Secreted protein acidic and rich in cysteine Ca binding region Provide feedback
The SPARC_Ca_bdg domain of Secreted Protein Acidic and Rich in Cysteine is responsible for the anti-spreading activity of human urothelial cells. It is rich in alpha-helices. This extracellular calcium-binding domain contains two EF-hands that each coordinates one Ca2+ ion, forming a helix-loop-helix structure that not only drives the conformation of the protein but is also necessary for biological activity. The anti-spreading activity was dependent on the coordination of Ca2+ by a Glu residue at the Z position of EF-hand 2 [1].
Literature references
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Delostrinos CF, Hudson AE, Feng WC, Kosman J, Bassuk JA; , J Cell Physiol. 2006;206:211-220.: The C-terminal Ca2+-binding domain of SPARC confers anti-spreading activity to human urothelial cells. PUBMED:16121393 EPMC:16121393
Internal database links
SCOOP: | Dockerin_1 DUF5580 EF-hand_1 EF-hand_11 EF-hand_4 EF-hand_5 EF-hand_6 EF-hand_7 EF-hand_8 EF-hand_9 EFhand_Ca_insen |
Similarity to PfamA using HHSearch: | EF-hand_5 EF-hand_5 EF-hand_7 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR019577
This entry represents the calcium-binding domain found in SPARC (Secreted Protein Acidic and Rich in Cysteine) and Testican (also known as SPOCK; or SParc/Osteonectin, Cwcv and Kazal-like domains) proteins. SPARC proteins are down-regulated in various tumours and may have a tumour-suppressor function [PUBMED:18459035, PUBMED:17325739]. Testican-3 appears to be a novel regulator that reduces the activity of matrix metalloproteinase (MMP) in adult T-cell leukemia (ATL) [PUBMED:19144404].
This cysteine-rich domain is responsible for the anti-spreading activity of human urothelial cells. This extracellular calcium-binding domain is rich in alpha-helices and contains two EF-hands that each coordinates one Ca2+ ion, forming a helix-loop-helix structure that not only drives the conformation of the protein but is also necessary for biological activity. The anti-spreading activity was dependent on the coordination of Ca2+ by a Glu residue at the Z position of EF-hand 2 [PUBMED:16121393].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | calcium ion binding (GO:0005509) |
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 EF_hand (CL0220), which has the following description:
The EF hand is a calcium binding domain found in a wide variety of proteins [1].
The clan contains the following 30 members:
Ca_chan_IQ Caleosin Cbl_N2 Cullin_binding DAG_kinase_N Dockerin_1 EF-hand_1 EF-hand_10 EF-hand_11 EF-hand_12 EF-hand_13 EF-hand_14 EF-hand_2 EF-hand_3 EF-hand_4 EF-hand_5 EF-hand_6 EF-hand_7 EF-hand_8 EF-hand_9 EF-hand_like EF_assoc_2 EFhand_Ca_insen Internalin_N IQ IQCJ-SCHIP1 NADPH_Ox p25-alpha S_100 SPARC_Ca_bdgAlignments
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 (20) |
Full (2436) |
Representative proteomes | UniProt (4124) |
NCBI (12121) |
Meta (13) |
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RP15 (357) |
RP35 (727) |
RP55 (1574) |
RP75 (2445) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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Seed (20) |
Full (2436) |
Representative proteomes | UniProt (4124) |
NCBI (12121) |
Meta (13) |
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RP15 (357) |
RP35 (727) |
RP55 (1574) |
RP75 (2445) |
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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: | Pfam-B_3882 (release 22.0), PROSITE_PS00613 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 20 |
Number in full: | 2436 |
Average length of the domain: | 110.80 aa |
Average identity of full alignment: | 27 % |
Average coverage of the sequence by the domain: | 28.33 % |
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: | 113 | ||||||||||||
Family (HMM) version: | 10 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 SPARC_Ca_bdg domain has been found. There are 8 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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