Summary: Auxin binding protein
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Auxin binding protein Edit Wikipedia article
Auxin binding protein | |||||||||
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![]() crystal structure of auxin-binding protein 1 in complex with 1-naphthalene acetic acid
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Identifiers | |||||||||
Symbol | Auxin_BP | ||||||||
Pfam | PF02041 | ||||||||
Pfam clan | CL0029 | ||||||||
InterPro | IPR000526 | ||||||||
SCOP | 1lr5 | ||||||||
SUPERFAMILY | 1lr5 | ||||||||
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In molecular biology, the auxin binding protein family is a family of proteins which bind auxin.[1] They are located in the lumen of the endoplasmic reticulum (ER). The primary structure of these proteins contains an N-terminal hydrophobic leader sequence of 30-40 amino acids, which could represent a signal for translocation of the protein to the ER.[2][3] The mature protein comprises around 165 residues, and contains a number of potential N-glycosylation sites. In vitro transport studies have demonstrated co-translational glycosylation.[3] Retention within the lumen of the ER correlates with an additional signal located at the C terminus, represented by the sequence Lys-Asp-Glu-Leu, known to be responsible for preventing secretion of proteins from the lumen of the ER in eukaryotic cells.[2][3]
References
- ^ Woo EJ, Marshall J, Bauly J, Chen JG, Venis M, Napier RM, et al. (2002). "Crystal structure of auxin-binding protein 1 in complex with auxin.". EMBO J. 21 (12): 2877–85. doi:10.1093/emboj/cdf291. PMC 126050
. PMID 12065401.
- ^ a b Hesse T, Feldwisch J, Balshusemann D, Bauw G, Puype M, Vandekerckhove J, Lobler M, Klambt D, Schell J, Palme K (September 1989). "Molecular cloning and structural analysis of a gene from Zea mays (L.) coding for a putative receptor for the plant hormone auxin". EMBO J. 8 (9): 2453–61. PMC 401229
. PMID 2555179.
- ^ a b c Palme K, Hesse T, Campos N, Garbers C, Yanofsky MF, Schell J (February 1992). "Molecular analysis of an auxin binding protein gene located on chromosome 4 of Arabidopsis". Plant Cell. 4 (2): 193–201. doi:10.1105/tpc.4.2.193. PMC 160120
. PMID 1321684.
This article incorporates text from the public domain Pfam and InterPro IPR000526
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
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.
Auxin binding protein Provide feedback
No Pfam abstract.
Internal database links
SCOOP: | AraC_binding CENP-C_C Cupin_1 Cupin_2 Cupin_3 DMSP_lyase MannoseP_isomer |
Similarity to PfamA using HHSearch: | Cupin_2 |
External database links
PRINTS: | PR00655 |
SCOP: | 1lr5 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000526
Auxin binding protein is located in the lumen of the endoplasmic reticulum (ER). The primary structure contains an N-terminal hydrophobic leader sequence of 30-40 amino acids, which could represent a signal for translocation of the protein to the ER [PUBMED:2555179, PUBMED:1321684]. The mature protein comprises around 165 residues, and contains a number of potential N-glycosylation sites. In vitro transport studies have demonstrated co-translational glycosylation [PUBMED:1321684]. Retention within the lumen of the ER correlates with an additional signal located at the C terminus, represented by the sequence Lys-Asp-Glu-Leu, known to be responsible for preventing secretion of proteins from the lumen of the ER in eukaryotic cells [PUBMED:2555179, PUBMED:1321684].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | auxin binding (GO:0010011) |
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 Cupin (CL0029), which has the following description:
This clan represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). The cupin fold is found in a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.
The clan contains the following 65 members:
2OG-Fe_Oxy_2 2OG-FeII_Oxy 2OG-FeII_Oxy_2 2OG-FeII_Oxy_3 2OG-FeII_Oxy_4 2OG-FeII_Oxy_5 3-HAO AIM24 AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox AUDH_Cupin Auxin_BP CDO_I CENP-C_C cNMP_binding CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_4 Cupin_5 Cupin_6 Cupin_7 Cupin_8 DIOX_N DMSP_lyase dTDP_sugar_isom DUF1479 DUF1971 DUF386 DUF4437 DUF4867 DUF5070 Ectoine_synth ERG2_Sigma1R EutQ FdtA FTO_NTD GPI HgmA HutD JmjC JmjN KduI Lyx_isomer MannoseP_isomer Ofd1_CTDD Oxygenase-NA PCO_ADO PhyH Pirin Pirin_C Pirin_C_2 PMI_typeI Popeye Pox_C4_C10 Ppnp TauD Tet_JBP Ureidogly_lyase VIT VIT_2Alignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
View options
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.
Seed (3) |
Full (229) |
Representative proteomes | UniProt (432) |
NCBI (1927) |
Meta (50) |
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RP15 (17) |
RP35 (118) |
RP55 (184) |
RP75 (232) |
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Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
Seed (3) |
Full (229) |
Representative proteomes | UniProt (432) |
NCBI (1927) |
Meta (50) |
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RP15 (17) |
RP35 (118) |
RP55 (184) |
RP75 (232) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
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.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | IPR000526 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Mian N |
Number in seed: | 3 |
Number in full: | 229 |
Average length of the domain: | 141.30 aa |
Average identity of full alignment: | 55 % |
Average coverage of the sequence by the domain: | 73.07 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 167 | ||||||||||||
Family (HMM) version: | 17 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
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Interactions
There is 1 interaction for this family. More...
Auxin_BPStructures
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 Auxin_BP domain has been found. There are 8 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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