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102  structures 3245  species 0  interactions 7333  sequences 81  architectures

Family: Dabb (PF07876)

Summary: Stress responsive A/B Barrel Domain

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Stress responsive A/B Barrel Domain Provide feedback

The function of this family is unknown, but it is upregulated in response to salt stress in Populus balsamifera ([1]). It is also found at the C-terminus of an fructose 1,6-bisphosphate aldolase from Hydrogenophilus thermoluteolus (Q9ZA13; [2]). Q93NG5 is found in the pA01 plasmid, which encodes genes for molybdopterin uptake and degradation of plant alkaloid nicotine. The structure of one has been solved (Q9LUV2) and the domain forms an a/b barrel dimer ([3]). Although there is a clear duplication within the domain it is not obviously detectable in the sequence.

Literature references

  1. Gu R, Fonseca S, Puskas LG, Hackler L Jr, Zvara A, Dudits D, Pais MS; , Tree Physiol 2004;24:265-276.: Transcript identification and profiling during salt stress and recovery of Populus euphratica. PUBMED:14704136 EPMC:14704136

  2. Hayashi NR, Terazono K, Kodama T, Igarashi Y; , Biosci Biotechnol Biochem 2000;64:61-71.: Structure of ribulose 1,5-bisphosphate carboxylase/oxygenase gene cluster from a thermophilic hydrogen-oxidizing bacterium, Hydrogenophilus thermoluteolus, and phylogeny of the fructose 1,6-bisphosphate aldolase encoded by cbbA in the cluster. PUBMED:10705449 EPMC:10705449

  3. Lytle BL, Peterson FC, Kjer KL, Frederick RO, Zhao Q, Thao S, Bingman C, Johnson KA, Phillips GN Jr, Volkman BF; , J Biomol NMR 2004;28:397-400.: Structure of the hypothetical protein At3g17210 from Arabidopsis thaliana. PUBMED:14872131 EPMC:14872131

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013097

The stress-response A/B barrel domain is found in a class of stress-response proteins in plants. It is also found in some bacterial fructose-bisphosphate aldolase such as at the C terminus of a fructose 1,6-bisphosphate aldolase from Hydrogenophilus thermoluteolus ( SWISSPROT ) [ PUBMED:10705449 ]. SWISSPROT is found in the pA01 plasmid, which encodes genes for molybdopterin uptake and degradation of plant alkaloid nicotine.

The stress-response A/B barrel domain forms a very stable dimer. This dimer belongs to the superfamily of dimeric alpha+beta barrels in which the two beta-sheets form a beta-barrel. The two molecules in the dimer are related by a 2-fold axis parallel to helix H1 and beta-strands B3 and B4. C-terminal residues extending from the beta4 strand of each monomer wrap around and connect with the beta2 strand and alpha1 helix of the opposing monomer to form the dimer interface [ PUBMED:15364906 , PUBMED:15213437 , PUBMED:15371455 ].The outer surface of the beta-sheets of the two molecules forms a beta-barrel-like structure defining a central pore.

The function of the stress-response A/B barrel domain is unknown [ PUBMED:15364906 , PUBMED:15213437 , PUBMED:15371455 ], but it is upregulated in response to salt stress in Populus balsamifera (balsam poplar) [ PUBMED:14704136 ].

Some proteins known to contain a stress response A/B barrel domain are listed below:

- Arabidopsis thaliana At3g17210

- Arabidopsis thaliana At5g22580

-Populus tremula stable protein 1 (SP-1)(Populus species), a thermostable stress-responsive protein.

- Pseudomonas hydrogenothermophila fructose 1,6-bisphosphate aldolase (cbbA).

The structure of one of these proteins has been solved ( SWISSPROT ) and the domain forms an alpha-beta barrel dimer [ PUBMED:14872131 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Dim_A_B_barrel (CL0032), which has the following description:

This superfamily of proteins possess a Ferredoxin-like fold. Pairs of these assemble into a beta barrel. The function of this barrel is quite varied and includes Muconolactone isomerase as well as monooxygenases.

The clan contains the following 28 members:

ABM AsnC_trans_reg AsnC_trans_reg2 Chalcone_N Chlor_dismutase Cyclase_polyket Dabb Dehydratase_hem DUF1330 DUF1428 DUF3291 DUF4188 DUF4242 DUF4937 Dyp_perox EthD FtsX_ECD GYD HapK MIase MmlI NapD NIPSNAP rhaM SchA_CurD SOR YCII ydhR


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Curation and family details

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Seed source: Yeats C
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Yeats C
Number in seed: 38
Number in full: 7333
Average length of the domain: 96.40 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 75.39 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.2 21.2
Trusted cut-off 21.2 21.2
Noise cut-off 21.1 21.1
Model length: 97
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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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 Dabb domain has been found. There are 102 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 sequence.

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