domain annotation of Trimeric Autotransporter Adhesins


Domains from the main daTAA database:


Domain name


Description

Neck

Neck sequence is an example of connector domain. As a connector, it nevers is found next to itself. It joins beta structures with coiled-coils (in the direction from N- to C-terminus only). This domain has two flavors, differing by insertion/deletion of three aminoacids in the central part (forming loop). Despite small length, it is very conserved and found in many proteobacterial species and also in few fusobacterial adhesins containing membrane anchor of trimeric autotransporters.

DALL-1

One of the flavors of DALL motif, a distinct connector domain between coiled-coil and heads (or often neck).

DALL-2

One of the flavors of DALL motif, a distinct connector domain between coiled-coil and heads (or often neck).

DALL-3

One of the flavors of DALL motif, a distinct connector domain between coiled-coil and heads (or often neck).

ISneck1

Neck with a folded insertion. Structure known thanks to solved head of Hia protein (PDB: 1s7m).

HANS

HANS connector

ISneck2

Neck with an insertion. In opposite to the ISneck1 domain, insertion does not seem to form a defined secondary structure (it is shorter).

Membrane anchor of autotransporter adhesins

This pore-shaped domain is the defining motif for the family, as its the only domain present in all TAAs. It is located mostly at the strict C-terminus of the protein, and exports the remaining parts out of the cell. After the export, the pore is occluded by a trimeric coiled-coil. PDB code for this structure: 2gr7 and 2gr8.

Autotransporter signal peptide

Conserved signal peptide present in autotransporter trimeric adhesins but also in other autotransporter adhesins (like single chain AIDA).

Trp ring

A distinctive feature of this domain is a ring of highly conserved tryptophanes. These residues seem to stabilize the whole domain at the transition between preceding coiled-coil and the domains beta-meander. Structure of this domain was first solved in the Hia adhesin from Haemophilus influenzae. Frequent neighbour of this domain is GIN.

GIN

One of the all-beta domains. It forms beta-prism in which each wall is composed of one chain. Often preceded by Trp-ring domain and in most cases followed by neck sequence.

FxG

Domain present mostly in Moraxella and Xylella adhesins. PFAM has a limited alignment containing only Xylella proteins.

HIN1

Head insert motif - first flavor. Defined by sequence GYDP and its variations.

Ylhead

YadA-like head domain. Forms a beta-roll. Present in most of the TAA family. Structure known thanks to solved head of YadA adhesin.

HIN2

Head insert motif, second flavor. Defined by FxG motif.

FGG

FGG is a domain of the stalk. It forms a coiled-coil with a beta-hairpin insert in the middle (structure is soon to be published). It occurs immediately after the neck sequence, and often is followed by one of DALL motifs.

Right-handed stalk

Right handed coiled-coil form a separate group of TAA stalks. Usually, they are not recognized by coiled-coil prediction software, such as Marcoil or COILS.
One of the most distinct right-handed stalks is a YTD motif. Its length is around 15 aminoacids long, but we observe few more flavors of this motif including, 23 and 37 AA long.


Domains from the beta database: (subject to testing and further analysis)



Domain name


Description

conGN

Possible neck-like beta-to-alpha connector.

YDD

YDD from Burkholderia

KG

KG, various species

VVYYT

VVYYT mainly Haemophilus

NIKE

Nike

GANG

Unidentified domain

TTT

TTT newly found