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21  structures 1  species 1  interaction 8  sequences 1  architecture

Family: AFP (PF02420)

Summary: Insect antifreeze protein repeat

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This is the Wikipedia entry entitled "Antifreeze protein". More...

Antifreeze protein Edit Wikipedia article

Insect antifreeze protein
PDB 1l1i EBI.jpg
Structure of the Tenebrio molitor beta-helical antifreeze protein[1]
Identifiers
Symbol AFP
Pfam PF02420
InterPro IPR003460
SCOP 1ezg
SUPERFAMILY 1ezg
Choristoneura fumiferana antifreeze protein (CfAFP)
PDB 1m8n EBI.jpg
Structure of Choristoneura fumiferana (spruce budworm) beta-helical antifreeze protein[2]
Identifiers
Symbol CfAFP
Pfam PF05264
InterPro IPR007928
SCOP 1m8n
SUPERFAMILY 1m8n
OPM superfamily 392
OPM protein 1l0s

Antifreeze proteins (AFPs) or ice structuring proteins (ISPs) refer to a class of polypeptides produced by certain vertebrates, plants, fungi and bacteria that permit their survival in subzero environments. AFPs bind to small ice crystals to inhibit growth and recrystallization of ice that would otherwise be fatal.[3] There is also increasing evidence that AFPs interact with mammalian cell membranes to protect them from cold damage. This work suggests the involvement of AFPs in cold acclimatization.[4]

Non-colligative properties

Unlike the widely used automotive antifreeze, ethylene glycol, AFPs do not lower freezing point in proportion to concentration.[citation needed] Rather, they work in a noncolligative manner. This phenomenon allows them to act as an antifreeze at concentrations 1/300th to 1/500th of those of other dissolved solutes. Their low concentration minimizes their effect on osmotic pressure.[4] The unusual properties of AFPs are attributed to their affinity for specific ice crystal surfaces.[5]

Thermal hysteresis

AFPs create a difference betw

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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.

Insect antifreeze protein repeat Provide feedback

This family of extracellular proteins is involved in stopping the formation of ice crystals at low temperatures. The proteins are composed of a 12 residue repeat that forms a structural repeat. The structure of the repeats is a beta helix [1]. Each repeat contains two cys residues that form a disulphide bridge.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003460

Antifreeze proteins (AFPs) are a class of proteins that are able to bind to and inhibit the growth of macromolecular ice, thereby permitting an organism to survive subzero temperatures by decreasing the probability of ice nucleation in their bodies [PUBMED:15291806]. These proteins have been characterised from a variety of organisms, including fish, plants, bacteria, fungi and arthropods. This entry represents insect AFPs of the type found in Tenebrio molitor (Yellow mealworm) and in Dendroides canadensis (Pyrochroid beetle).

The structure of these AFPs consists of a right-handed beta-helix with 12 residues per coil. Each 12 residue-repeat contains two cys residues that form a disulphide bridge. The beta-helices of insect AFPs present a highly rigid array of threonine residues and bound water molecules that can effectively mimic the ice lattice. As such, beta-helical AFPs provide a more effective coverage of the ice surface compared to the alpha-helical fish AFPs [PUBMED:10917536].

A second insect antifreeze from Choristoneura fumiferana (Spruce budworm) (INTERPRO) also consists of beta-helices, however in these proteins the helices form a left-handed twist; these proteins show no sequence homology to the current entry, but may act by a similar mechanism. The beta-helix motif may be used as an AFP structural motif in non-homologous proteins from other (non-fish) organisms as well.

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

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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.

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(9)
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(541)
NCBI
(548)
Meta
(0)
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()
RP35
(8)
RP55
(8)
RP75
(8)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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  Seed
(9)
Full
(8)
Representative proteomes UniProt
(541)
NCBI
(548)
Meta
(0)
RP15
()
RP35
(8)
RP55
(8)
RP75
(8)
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  Seed
(9)
Full
(8)
Representative proteomes UniProt
(541)
NCBI
(548)
Meta
(0)
RP15
()
RP35
(8)
RP55
(8)
RP75
(8)
Raw Stockholm Download   Download     Download   Download   Download   Download   Download    
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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.

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Curation and family details

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Curation View help on the curation process

Seed source: [1]
Previous IDs: none
Type: Repeat
Author: Bateman A
Number in seed: 9
Number in full: 8
Average length of the domain: 10.20 aa
Average identity of full alignment: 85 %
Average coverage of the sequence by the domain: 23.84 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 36.5 2.0
Trusted cut-off 45.1 3.6
Noise cut-off 22.9 1.9
Model length: 12
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

AFP

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 AFP domain has been found. There are 21 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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