Elongation Factors

What InterPro Tells Us

P02994 Yeast Elongation Factor EF1A

InterPro Domain Architecture

InterPro Entry	Signatures	Graphical Match	Method Name
IPR000795	PF00009		GTP_EFTU
IPR000795	PR00315		ELONGATNFCT
IPR000795	PS00301		EFACTOR_GTP
IPR004160	PF03143		GTP_EFTU_D3
IPR004161	PF03144		GTP_EFTU_D2
IPR004539	TIGR00483		EF-1_alpha
IPR009000	SSF50447		Translat_factor
IPR009001	SSF50465		Elong_init_C
Structural Features
1f60	1f60A
2.40.30.10.13	1f60A2
2.40.30.10.2	1f60A3
3.40.50.300.16	1f60A1
b.43.3.1	d1f60a1
b.44.1.1	d1f60a2
c.37.1.8	d1f60a3

From the graphical match above, you can see that the signatures are all grouped into six InterPro entries for yeast elongation factor EF1A. InterPro entries group together all the signatures that represent the same sequence found in the same set of proteins. These entries provide a family grouping of EF1A proteins, as well as subdividing EF1A into three constituent domains.

FAMILY Entries

Ø IPR004539: Translation elongation factor EF1A family, represented by one signature: TIGR00483 (TIGRFAM).

DOMAIN Entries

Ø IPR000795: GTP-binding domain, represented by three signatures: PF00009 (PFAM), PR00315 (PRINTS), and PS00301 (PROSITE).

Ø IPR009000: Translation factor domain, represented by one signature: SSF50447 (SUPERFAMILY).

Ø IPR004161: EF1A domain 2, represented by one signature: PF03144 (PFAM).

Ø IPR009001: C-terminal domain of EF1A and Initiation Factor IFg, represented by one signature: SSF50465 (SUPERFAMILY).

Ø IPR004160: C-terminal domain of EF1A, represented by one signature: PF03143 (PFAM).

The two signatures for the middle domain, SSF50447 (IPR009000) and PF03144 (IPR004161), are related to one another as they cover the same sequence, but hit overlapping sets of proteins and therefore form a hierarchical relationship. The entry IPR009000 is top of the hierarchy as it hits the most proteins, including EF1A and other translation factors. It has one ‘child’ entry, IPR004161, which represents the same sequence, but which is restricted to EF1A proteins.

Similarly, the two signatures for the C-terminal domain, SSF50465 (IPR009001) and PF03143 (IPR004160), form a hierarchy, where IPR009001 is at the top, hitting the C-terminal domain of both elongation factor and initiation factor proteins, while its ‘child’ entry, IPR004160, hits the same sequence but only in elongation factor proteins.

The remaining seven 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 1f60A3 are derived from the PDB entry upon which they are based, here PDB entry 1f60, chain A, fragment 3). The graphical match for the PDB entry 1f60 displays the full length of the original PDB entry, here covering the entire protein. The CATH and SCOP entries breakdown the PDB data into its constituent domains based on structure, providing a structural classification for each domain and relating it to other structures in the PDB database. Both CATH and SCOP divide EF1A into three domains with the same boundaries as each other, and as the InterPro signatures above. These three domains are:

Ø N-terminal domain is represented by 3.40.50.300.16 (CATH) and c.37.1.8 (SCOP), and has a 3-layer beta/alpha/beta fold common to many P-loop containing NTP hydrolases, including several G-proteins, nucleotide kinases, sulphotransferases, phosphotransferases, amongst others.

Ø Middle domain is represented by 2.40.30.10.13 (CATH) and b.43.3.1 (SCOP), and has a beta-barrel fold common to both elongation factors and the ribosomal protein L3.

Ø C-terminal domain is represented by 2.40.30.10.2 (CATH) and b.44.1.1 (SCOP), and has a beta-barrel fold common to both elongation factors and initiation factors.

The N-terminal domain functions in binding GTP or GDP. Within this domain, switch 1 and switch 2 regions show significant local structural changes depending upon whether GTP or GDP is bound. The middle and C-terminal domains are held together in the same relative orientation, and appear to function as one rigid functional unit. Therefore, there are two functional units, domain I and domains II/III, which are separated from one another to facilitate conformational changes in the switch regions of domain I, as well as other conformational changes.

What the Structure Tells Us

Structures associated with various elongation factors 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 P02994). The AstexViewer® displays the PDB structure with the specific CATH or SCOP domain highlighted.

There are structures available for various elongation factors in the Protein Data Bank (PDB). A detailed description and visualisation of the structural features of these proteins can be found at the PDB ‘Molecule of the Month’. The crystallographic structures of various elongation factors have provided insight into the mechanism of protein elongation.

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