Green Fluorescent Protein
What InterPro Tells Us
P42212 Green Fluorescent Protein from Aequorea victoria
InterPro Domain Architecture
InterPro Entry |
Signatures |
Graphical Match |
Method Name |
|
IPR000786: |
PD013756
|
|
Green_fl_protein |
|
IPR000786: |
PR01229 |
|
GFLUORESCENT |
|
IPR009017: |
SSF54511 |
|
GFP_like |
|
IPR011584: |
PF01353 |
|
GFP |
|
Structural Features |
|
|
|
|
1q4e |
1q4eA |
|
|
|
2.40.155.10.1 |
1q4eA0 |
|
|
|
d.22.1.1 |
d1q4ea_
|
|
|
From the graphical match above, you can see that the signatures are grouped into three InterPro entries for green fluorescent protein from A. victoria. These entries give information about the domain architecture of the protein, as well as their evolutionary relationships.
The entry for
GFP, IPR000786, has two signatures: PD013756 from the ProDom database (obtained from
an alignment of twelve proteins, spanning multiple genera and including both
fluorescent proteins and chromoproteins), and PR01229 from the PRINTS database (an
eleven-element fingerprint derived from an initial alignment of five sequences;
the motifs were drawn from conserved regions in the alignment, and correspond to
secondary structural elements of the protein).
The entry IPR011584 represents GFP-related proteins,
and as such covers a wider range of proteins that includes those that are
related by sequence to GFP; this entry has one signature: PF01353 from the PFAM database (obtained from an
alignment of 10 proteins spanning several genera, and including both
fluorescent proteins and chromoproteins).
The remaining entry, IPR009017, has one signature, SSF54511 from the SUPERFAMILY database,
which represents GFP-like proteins. This
entry includes not only fluorescent protein, but also those proteins that share
a common structure with GFP such as the G2 domain of mouse nidogen-1. Nidogen is a component of basement
membranes, whose protein interactions contribute to the assembly and function
of the basement membrane. Nidogens are
neither fluorescent nor coloured, their G2 domain serving as a protein-binding
module. The G2 domain of nidogen
contains a beta-can structure that exhibits extraordinary similarity to GFP,
even though their sequences show only low sequence identity. The chromophore tripeptide in GFP is absent
in nidogen, the equivalent residues forming part of helix2. Furthermore, the highly conserved residues in
GFP required for chromophore formation are not conserved in nidogen. Nonetheless, the structure is similar enough
to suggest a common ancestral origin. It is possible that protein binding
constitutes the most ancient, pre-fluorescent function of the common ancestor
of GFPs and G2 domain-containing proteins.
In InterPro, these three entries are related to each other: IPR009017 (proteins with GFP-like structure) is the parent of IPR009017 (proteins related to GFP by sequence), which in turn is the parent of IPR000786 (GFP proteins). The different signatures are useful to gain an insight into the annotation of the protein, and to discern relationships with other proteins or domains within InterPro. From the InterPro entry you can find all the corresponding proteins in UniProt, a graphical representation of their overlap, the taxonomy of the entries, and any links to other families or domains in the database.
The remaining three entries in the table above give information on the structure of this protein, presenting known structural data from the structural database PDB (green stripe) and the structural classification databases CATH (pink stripe) and SCOP (black stripe) (the names such as d1q4ea_ are derived from the PDB entry upon which they are based, here PDB entry 1q4e, chain A). The graphical match for the PDB entry 1q4eA displays the full length of the original PDB entry, here covering almost the entire protein. The CATH and SCOP entries provide a structural classification of the domain: SCOP d1q4ea_ and CATH 1q4eA0 are both classed as b-sheets folded into a barrel around a central helix.
What the Structure tells us
Structures
associated with green fluorescent protein can be viewed using AstexViewer®,
which is linked from the Match Table via the logo 
on the InterPro page (please note, there is no link directly from
this page to the AstexViewer®, therefore you need to go to the link on the InterPro page for P42212).
The AstexViewer® displays the PDB structure with the specific CATH or
SCOP domain highlighted.
There are
structures available for various fluorescent proteins from different species in the
Protein Data Bank (PDB). These
structures reveal the beta-can structure of GFP that surrounds the
chromophore, and which is essential for fluorescence as a shield against
quenching agents. Despite the diversity
in chromophore structure between colour groups, all the proteins share this
beta-can structure. A detailed description and
visualisation of the structural features of amylases can be found at the PDB ‘Molecule of the Month’.
The crystallographic structures of different amylases have provided
insight into the mechanism of action of these important chromophores.