Summary: Importin beta binding domain
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Importin
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| mouse importin alpha-nucleoplasmin nls peptide complex | |||||||||
| Identifiers | |||||||||
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| Symbol | IBB | ||||||||
| Pfam | PF01749 | ||||||||
| Pfam clan | CL0020 | ||||||||
| InterPro | IPR002652 | ||||||||
| SCOP | 1bk5 | ||||||||
| SUPERFAMILY | 1bk5 | ||||||||
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| structure of the karyopherin beta2-ran gppnhp nuclear transport complex | |||||||||
| Identifiers | |||||||||
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| Symbol | IBN_N | ||||||||
| Pfam | PF03810 | ||||||||
| Pfam clan | CL0020 | ||||||||
| InterPro | IPR001494 | ||||||||
| SCOP | 1qbk | ||||||||
| SUPERFAMILY | 1qbk | ||||||||
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Importin is a type of protein that moves other protein molecules into the nucleus by binding to a specific recognition sequence, called the nuclear localization signal (NLS). Importin is classified as a karyopherin.[1][2]
Importin has two subunits, importin α and importin β. Members of the importin-beta family can bind and transport cargo by themselves, or can form heterodimers with importin-alpha. As part of a heterodimer, importin-beta mediates interactions with the pore complex, while importin-alpha acts as an adaptor protein to bind the nuclear localisation signal (NLS) on the cargo through the classical NLS import of proteins. The NLS-Importin α-Importin β trimer dissociates after binding to Ran GTP inside the nucleus.[3] Proteins can contain one (monopartite) or two (bipartite) NLS motifs. Importin-alpha contains several armadillo (ARM) repeats, which produce a curving structure with two NLS-binding sites, a major one close to the N terminus and a minor one close to the C terminus. Importin alpha also contains an N-terminal importin beta binding domain that contains an auto-regulatory region.[4] Importin-beta is a helicoidal molecule constructed from 19 HEAT repeats. Many nuclear pore proteins contain FG sequence repeats that can bind to HEAT repeats within importins, which is important for importin-beta mediated transport.[5][6]
Ran GTPase helps to control the unidirectional transfer of cargo. The cytoplasm contains primarily RanGDP and the nucleus RanGTP through the actions of RanGAP and RanGEF, respectively. In the nucleus, RanGTP binds to importin-beta within the importin/cargo complex, causing a conformational change in importin-beta that releases it from importin-alpha-bound cargo. The N-terminal importin-beta-binding (IBB) domain of importin-alpha contains an auto-regulatory region that mimics the NLS motif.[4] The release of importin-beta frees the auto-regulatory region on importin-alpha to loop back and bind to the major NLS-binding site, causing the cargo to be released.[7]
[edit] Human importin genes
- Importin: IPO4, IPO7, IPO8, IPO9, IPO11, IPO13
- Karyopherin-α: KPNA1, KPNA2, KPNA3, KPNA4, KPNA5, KPNA6
- Karyopherin-β: KPNB1
[edit] References
- ^ http://big.mcw.edu/display.php/1053.html
- ^ Görlich D, Prehn S, Laskey RA, Hartmann E (1994). "Isolation of a protein that is essential for the first step of nuclear protein import". Cell 79 (5): 767–78. doi:10.1016/0092-8674(94)90067-1. PMID 8001116.
- ^ Mattaj IW, Englmeier L (1998). "Nucleocytoplasmic transport: the soluble phase". Annu. Rev. Biochem. 67: 265–306. doi:10.1146/annurev.biochem.67.1.265. PMID 9759490.
- ^ a b Moroianu J, Blobel G, Radu A (1996). "The binding site of karyopherin alpha for karyopherin beta overlaps with a nuclear localization sequence.". Proc Natl Acad Sci U S A 93 (13): 6572–6. PMC 39066. PMID 8692858. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=39066.
- ^ Bayliss R, Littlewood T, Strawn LA, Wente SR, Stewart M (December 2002). "GLFG and FxFG nucleoporins bind to overlapping sites on importin-beta". J. Biol. Chem. 277 (52): 50597–606. doi:10.1074/jbc.M209037200. PMID 12372823.
- ^ Isgro TA, Schulten K (February 2007). "Association of nuclear pore FG-repeat domains to NTF2 import and export complexes". J. Mol. Biol. 366 (1): 330–45. doi:10.1016/j.jmb.2006.11.048. PMID 17161424.
- ^ Lange A, Mills RE, Lange CJ, Stewart M, Devine SE, Corbett AH (February 2007). "Classical nuclear localization signals: definition, function, and interaction with importin alpha". J. Biol. Chem. 282 (8): 5101–5. doi:10.1074/jbc.R600026200. PMID 17170104.
[edit] External links
This article incorporates text from the public domain Pfam and InterPro IPR002652 This article incorporates text from the public domain Pfam and InterPro IPR001494
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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.
Importin beta binding domain
This family consists of the importin alpha (karyopherin alpha), importin beta (karyopherin beta) binding domain. The domain mediates formation of the importin alpha beta complex; required for classical NLS import of proteins into the nucleus, through the nuclear pore complex and across the nuclear envelope. Also in the alignment is the NLS of importin alpha which overlaps with the IBB domain [4].
Literature references
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Conti E, Uy M, Leighton L, Blobel G, Kuriyan J; , Cell 1998;94:193-204.: Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin alpha. PUBMED:9695948
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Weis K; , Trends Biochem Sci 1998;23:185-189.: Importins and exportins: how to get in and out of the nucleus [published erratum appears in Trends Biochem Sci 1998 Jul;23(7):235] PUBMED:9612083
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Gorlich D; , EMBO J 1998;17:2721-2727.: Transport into and out of the cell nucleus. PUBMED:9582265
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Moroianu J, Blobel G, Radu A; , Proc Natl Acad Sci U S A 1996;93:6572-6576.: The binding site of karyopherin alpha for karyopherin beta overlaps with a nuclear localization sequence. PUBMED:8692858
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Gorlich D, Henklein P, Laskey RA, Hartmann E; , EMBO J 1996;15:1810-1817.: A 41 amino acid motif in importin-alpha confers binding to importin- beta and hence transit into the nucleus. PUBMED:8617226
Clan
This family is a member of clan TPR (CL0020), which has a total of 110 members.
External database links
| HOMSTRAD: | ARM |
| PANDIT: | PF01749 |
| Pseudofam: | PF01749 |
| SCOP: | 1bk5 |
| SYSTERS: | IBB |
This tab holds annotation information from the InterPro database.
InterPro entry IPR002652
The exchange of macromolecules between the nucleus and cytoplasm takes place through nuclear pore complexes within the nuclear membrane. Active transport of large molecules through these pore complexes require carrier proteins, called karyopherins (importins and exportins), which shuttle between the two compartments.
Members of the importin-alpha (karyopherin-alpha) family can form heterodimers with importin-beta. As part of a heterodimer, importin-beta mediates interactions with the pore complex, while importin-alpha acts as an adaptor protein to bind the nuclear localisation signal (NLS) on the cargo through the classical NLS import of proteins. Proteins can contain one (monopartite) or two (bipartite) NLS motifs. Importin-alpha contains several armadillo (ARM) repeats, which produce a curving structure with two NLS-binding sites, a major one close to the N terminus and a minor one close to the C terminus.
Ran GTPase helps to control the unidirectional transfer of cargo. The cytoplasm contains primarily RanGDP and the nucleus RanGTP through the actions of RanGAP and RanGEF, respectively. In the nucleus, RanGTP binds to importin-beta within the importin/cargo complex, causing a conformational change in importin-beta that releases it from importin-alpha-bound cargo. The N-terminal importin-beta-binding (IBB) domain of importin-alpha contains an auto-regulatory region that mimics the NLS motif [PUBMED:8692858]. The release of importin-beta frees the auto-regulatory region on importin-alpha to loop back and bind to the major NLS-binding site, causing the cargo to be released [PUBMED:17170104].
This entry represents the N-terminal IBB domain of importin-alpha that contains the auto-regulatory region.
More information about these proteins can be found at Protein of the Month: Importins [PUBMED:].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Cellular component | nuclear pore (GO:0005643) |
| nucleus (GO:0005634) | |
| cytoplasm (GO:0005737) | |
| Molecular function | protein transporter activity (GO:0008565) |
| Biological process | intracellular protein transport (GO:0006886) |
| protein import into nucleus (GO:0006606) |
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 TPR (CL0020), which contains the following 110 members:
Adaptin_N Apc3 Apc5 API5 Arm Arm_2 Avirulence BTAD CAS_CSE1 ChAPs CLASP_N Clathrin Clathrin-link Clathrin_propel Cnd1 Cnd3 Coatomer_E Cohesin_HEAT Cohesin_load CRM1_C Cse1 DNA_alkylation Drf_FH3 Drf_GBD DUF1822 DUF2225 DUF2435 DUF3385 DUF3458 DUF3808 DUF3856 EST1_DNA_bind FAT Foie-gras_1 GUN4 HAT HEAT HEAT_2 HEAT_EZ HEAT_PBS HemY_N IBB IBN_N IFRD KAP Leuk-A4-hydro_C LRV LRV_FeS MA3 MIF4G MIF4G_like MIF4G_like_2 Mo25 MRP-S27 NARP1 Neurochondrin Nro1 NSF Paf67 ParcG PC_rep PHAT PI3Ka PPP5 PPR PPR_1 PPR_2 PPR_3 Proteasom_PSMB PUF Rab5-bind Rapsyn_N RPN7 Sel1 SHNi-TPR SPO22 ST7 Suf SusD SusD-like SusD-like_2 SusD-like_3 Tcf25 TOM20_plant TPR_1 TPR_10 TPR_11 TPR_12 TPR_14 TPR_15 TPR_16 TPR_17 TPR_18 TPR_2 TPR_3 TPR_4 TPR_5 TPR_6 TPR_7 TPR_8 TPR_9 Upf2 V-ATPase_H_C V-ATPase_H_N Vac14_Fab1_bd Vitellogenin_N Vps39_1 W2 Xpo1 YfiOAlignments
There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...
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Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.
You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.
External links
MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.
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. 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 or full alignments.
Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.
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: | Pfam-B_544 (release 4.2) |
| Previous IDs: | none |
| Type: | Family |
| Author: | Bashton M, Bateman A |
| Number in seed: | 18 |
| Number in full: | 530 |
| Average length of the domain: | 92.30 aa |
| Average identity of full alignment: | 30 % |
| Average coverage of the sequence by the domain: | 18.65 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 97 | ||||||||||||
| Family (HMM) version: | 15 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
Archea
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Eukaryota
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Bacteria
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Other sequences
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Viruses
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Unclassified
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Viroids
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Unclassified sequence
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Structures
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 IBB domain has been found. There are 9 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 seqence.
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