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2  structures 53  species 0  interactions 290  sequences 4  architectures

Family: Granin (PF01271)

Summary: Granin (chromogranin or secretogranin)

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Granin Edit Wikipedia article

Granin (chromogranin or secretogranin)
PDB 1n2y EBI.jpg
Structure of SS-cyclized catestatin fragment from chromogranin A.[1]
Identifiers
Symbol Granin
Pfam PF01271
InterPro IPR001990
PROSITE PDOC00365
SCOP 1cfk
SUPERFAMILY 1cfk
OPM superfamily 328
OPM protein 1lv4

Granin (chromogranin and secretogranin) is a protein family of regulated secretory proteins ubiquitously found in the cores of amine and peptide hormone and neurotransmitter dense-core secretory vesicles.[2]

Function[edit]

Granins (chromogranins or secretogranins) are acidic proteins and are present in the secretory granules of a wide variety of endocrine and neuro-endocrine cells. The exact function(s) of these proteins is not yet settled but there is evidence that granins function as pro-hormones, giving rise to an array of peptide fragments for which autocrine, paracrine, and endocrine activities have been demonstrated in vitro and in vivo. The intracellular biochemistry of granins includes binding of Ca2+, ATP and catecholamines (epinephrine, norepinephrine) within the hormone storage vesicle core. There is also evidence that CgA, and perhaps other granins, regulate the biogenesis of dense-core secretory vesicles and hormone sequestration in neuroendocrine cells.

Structure[edit]

Apart from their subcellular location and the abundance of acidic residues (Asp and Glu), these proteins do not share many structural similarities. Only one short region, located in the C-terminal section, is conserved in all these proteins. Chromogranins and secretogranins together share a C-terminal motif, whereas chromogranins A and B share a region of high similarity in their N-terminal section; this region includes two cysteine residues involved in a disulfide bond.

Members[edit]

Chromogranins[edit]

chromogranin A
(parathyroid secretory protein 1)
Identifiers
Symbol CHGA
Alt. symbols CGA
Entrez 1113
HUGO 1929
OMIM 118910
RefSeq NM_001275
UniProt P10645
Other data
Locus Chr. 14 q32
chromogranin B
(secretogranin 1)
Identifiers
Symbol CHGB
Alt. symbols SCG1
Entrez 1114
HUGO 1930
OMIM 118920
RefSeq NM_001819
UniProt P05060
Other data
Locus Chr. 20 pter-p12

Secretogranins[edit]

secretogranin II
(chromogranin C)
Identifiers
Symbol SCG2
Alt. symbols CHGC, SgII
Entrez 7857
HUGO 10575
OMIM 118930
RefSeq NM_003469
UniProt P13521
Other data
Locus Chr. 2 q35-q36
secretogranin III
(FLJ90833)
Identifiers
Symbol SCG3
Alt. symbols SGIII
Entrez 29106
HUGO 13707
OMIM 611796
RefSeq NM_013243
UniProt Q8WXD2
Other data
Locus Chr. 15 q21.3
secretogranin V
(7B2 protein)
Identifiers
Symbol SCG5
Alt. symbols SGNE1
Entrez 6447
HUGO 10816
OMIM 173120
RefSeq NM_003020
UniProt P05408
Other data
Locus Chr. 15 q13-q14

Two other proteins (secretogranin IV and VI) are also proposed to belong to the granins on the basis of their physico-chemical properties.

References[edit]

  1. ^ Preece NE, Nguyen M, Mahata M, et al. (April 2004). "Conformational preferences and activities of peptides from the catecholamine release-inhibitory (catestatin) region of chromogranin A". Regul. Pept. 118 (1-2): 75–87. doi:10.1016/j.regpep.2003.10.035. PMID 14759560. 
  2. ^ Huttner WB, Gerdes HH, Rosa P (January 1991). "The granin (chromogranin/secretogranin) family". Trends Biochem. Sci. 16 (1): 27–30. doi:10.1016/0968-0004(91)90012-K. PMID 2053134. 

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR001990


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.

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No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001990

Granins (chromogranins or secretogranins) [PUBMED:2053134] are a family of acidic proteins present in the secretory granules of a wide variety of endocrine and neuro-endocrine cells. The exact function(s) of these proteins is not yet known but they seem to be the precursors of biologically active peptides and/or they may act as helper proteins in the packaging of peptide hormones and neuropeptides. Apart from their subcellular location and the abundance of acidic residues (Asp and Glu), these proteins do not share many structural similarities. Only one short region, located in the C-terminal section, is conserved in all these proteins.

Chromogranins and secretogranins together share a C-terminal motif, whereas chromogranins A and B share a region of high similarity in their N-terminal section; this region includes two cysteine residues involved in a disulphide bond.

Gene Ontology

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Domain organisation

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(9)
Full
(290)
Representative proteomes NCBI
(264)
Meta
(0)
RP15
(4)
RP35
(11)
RP55
(33)
RP75
(101)
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Format an alignment

  Seed
(9)
Full
(290)
Representative proteomes NCBI
(264)
Meta
(0)
RP15
(4)
RP35
(11)
RP55
(33)
RP75
(101)
Alignment:
Format:
Order:
Sequence:
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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
(9)
Full
(290)
Representative proteomes NCBI
(264)
Meta
(0)
RP15
(4)
RP35
(11)
RP55
(33)
RP75
(101)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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: Prosite
Previous IDs: none
Type: Family
Author: Finn RD, Bateman A
Number in seed: 9
Number in full: 290
Average length of the domain: 329.00 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 89.82 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 27.7 26.3
Noise cut-off 23.8 24.9
Model length: 586
Family (HMM) version: 12
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 Granin domain has been found. There are 2 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 seqence.

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