Summary: Histone RNA hairpin-binding protein RNA-binding domain
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|, HBP, stem-loop binding protein|
SLBP has been cloned from humans, C. elegans, D. melanogaster, X. laevis, and sea urchins. The full length human protein has 270 amino acids (31 kDa) with a centrally located RNA binding domain (RBD). The 75 amino acid RBD is well conserved across species, however the remainder of SLBP is highly divergent in most organisms and not homologous to any other protein in the eukaryotic genomes.
This gene encodes a protein that binds to the histone 3' UTR stem-loop structure in replication-dependent histone mRNAs. Histone mRNAs do not contain introns or polyadenylation signals, and are processed by a single endonucleolytic cleavage event downstream of the stem-loop. The stem-loop structure is essential for efficient processing of the histone pre-mRNA but this structure also controls the transport, translation and stability of histone mRNAs. SLBP expression is regulated during S-phase of the cell cycle, increasing more than 10-fold during the latter part of G1.
All SLBP proteins are capable of forming a highly stable complex with histone stem-loop RNA. Complex formation with the histone mRNA stem-loop is achieved by a novel three-helix bundle fold. SLBP proteins also recognize the tetraloop structure of the histone hairpin, the base of the stem, and the 5' flanking region. The crystal structure of human SLBP in complex with the stem-loop RNA as well as the exonuclease Eri1 reveals that the Arg181 residue of SLBP specifically interacts with the second guanine base in the RNA stem. The rest of the protein is intrinsically disordered in fruit-flies as well as in humans. A unique feature of the SLBP RBD is that it is phosphorylated in its RNA binding domain at the Thr171 residue. The SLBP RBD also undergoes proline isomerization about this sequence and is a substrate for the prolyl isomerase Pin1. The N-terminal domain of human SLBP is required for translation activation of histone mRNAs via its interaction with SLIP1. SLBP also interacts with the CBP80 associated protein CTIF to facilitate rapid degradation of histone mRNAs. SLBP is a phosphoprotein and besides T171, it is also phosphorylated at Ser7, Ser20, Ser23, Thr60, Thr61 in mammalian cells. The phosphorylation at Thr60 is mediated by CK2 and Thr61 is by Cyclin A/Cdk1.
- GRCh38: Ensembl release 89: ENSG00000163950 - Ensembl, May 2017
- GRCm38: Ensembl release 89: ENSMUSG00000004642 - Ensembl, May 2017
- "Human PubMed Reference:".
- "Mouse PubMed Reference:".
- Martin F, Schaller A, Eglite S, Schumperli D, Muller B (Mar 1997). "The gene for histone RNA hairpin binding protein is located on human chromosome 4 and encodes a novel type of RNA binding protein". EMBO J. 16 (4): 769–78. doi:10.1093/emboj/16.4.769. PMC . PMID 9049306.
- McCombie WR, Martin-Gallardo A, Gocayne JD, FitzGerald M, Dubnick M, Kelley JM, Castilla L, Liu LI, Wallace S, Trapp S (August 1992). "Expressed genes, Alu repeats and polymorphisms in cosmids sequenced from chromosome 4p16.3". Nature Genetics. 1 (5): 348–53. doi:10.1038/ng0892-348. PMID 1338771.
- "Entrez Gene: SLBP stem-loop (histone) binding protein".
- Dazhi Tan; William F. Marzluff; Zbigniew Dominski; Liang Tong (Jan 2013). "Structure of Histone mRNA Stem-Loop, Human Stem-Loop Binding Protein, and 3′hExo Ternary Complex". Science. 339 (6117): 318–321. doi:10.1126/science.1228705. PMC . PMID 23329046.
- Choe J, Mi Kim K, Park S, Kyung Lee Y, Song O-K, Kim MK, Lee BG, Song HK, Kim YK (2013). "Rapid degradation of replication-dependent histone mRNAs largely occurs on mRNAs bound by nuclear cap-binding proteins 80 and 20". Nucleic Acids Research. 41 (2): 1307–1318. doi:10.1093/nar/gks1196.
- Bansal N, Zhang M, Bhaskar A, Itotia P, Lee E, Shlyakhtenko LS, Lam TT, Fritz A, Berezney R, Lyubchenko YL, Stafford WF, Thapar R (January 2013). "Assembly of the SLIP1-SLBP complex on histone mRNA requires heterodimerization and sequential binding of SLBP followed by SLIP1". Biochemistry. 52 (3): 520–536. doi:10.1021/bi301074r. PMC . PMID 23286197.
- Martin L, Meier M, Lyons SM, Sit RV, Marzluff WF, Quake SR, Chang HY (December 2012). "Systematic reconstruction of RNA functional motifs with high-throughput microfluidics". Nature Methods. 9 (12): 1192–4. doi:10.1038/nmeth.2225.
- Krishnan N, Lam TT, Fritz A, Rempinski D, O'Loughlin K, Minderman H, Berezney R, Marzluff WF, Thapar R (November 2012). "The Prolyl Isomerase Pin1 Targets Stem-Loop Binding Protein (SLBP) To Dissociate the SLBP-Histone mRNA Complex Linking Histone mRNA Decay with SLBP Ubiquitination". Mol. Cell. Biol. 32 (21): 4306–22. doi:10.1128/MCB.00382-12. PMID 22907757.
- Zhang M, Lam TT, Tonelli M, Marzluff WF, Thapar R (April 2012). "Interaction of the histone mRNA hairpin with stem-loop binding protein (SLBP) and regulation of the SLBP-RNA complex by phosphorylation and proline isomerization". Biochemistry. 51 (15): 3215–31. doi:10.1021/bi2018255. PMID 22439849.
- Borchers CH, Thapar R, Petrotchenko EV, Torres MP, Speir JP, Easterling M, Dominski Z, Marzluff WF (February 2006). "Combined top-down and bottom-up proteomics identifies a phosphorylation site in stem-loop-binding proteins that contributes to high-affinity RNA binding". Proc. Natl. Acad. Sci. U.S.A. 103 (9): 3094–9. doi:10.1073/pnas.0511289103. PMC . PMID 16492733.
- Thapar R, Marzluff WF, Redinbo MR (July 2004). "Electrostatic contribution of serine phosphorylation to the Drosophila SLBP--histone mRNA complex". Biochemistry. 43 (29): 9401–12. doi:10.1021/bi036315j. PMID 15260483.
- Thapar R, Mueller GA, Marzluff WF (July 2004). "The N-terminal domain of the Drosophila histone mRNA binding protein, SLBP, is intrinsically disordered with nascent helical structure". Biochemistry. 43 (29): 9390–400. doi:10.1021/bi036314r. PMID 15260482.
- Wang ZF, Whitfield ML, Ingledue TC, Dominski Z, Marzluff WF (December 1996). "The protein that binds the 3' end of histone mRNA: a novel RNA-binding protein required for histone pre-mRNA processing". Genes Dev. 10 (23): 3028–40. doi:10.1101/gad.10.23.3028. PMID 8957003.
- Dominski Z, Zheng LX, Sanchez R, Marzluff WF (May 1999). "Stem-loop binding protein facilitates 3'-end formation by stabilizing U7 snRNP binding to histone pre-mRNA". Mol. Cell. Biol. 19 (5): 3561–70. doi:10.1128/mcb.19.5.3561. PMC . PMID 10207079.
- Whitfield ML, Zheng LX, Baldwin A, Ohta T, Hurt MM, Marzluff WF (June 2000). "Stem-loop binding protein, the protein that binds the 3' end of histone mRNA, is cell cycle regulated by both translational and posttranslational mechanisms". Mol. Cell. Biol. 20 (12): 4188–98. doi:10.1128/MCB.20.12.4188-4198.2000. PMC . PMID 10825184.
- Dominski Z, Erkmann JA, Greenland JA, Marzluff WF (March 2001). "Mutations in the RNA binding domain of stem-loop binding protein define separable requirements for RNA binding and for histone pre-mRNA processing". Mol. Cell. Biol. 21 (6): 2008–17. doi:10.1128/MCB.21.6.2008-2017.2001. PMC . PMID 11238936.
- Allard P, Champigny MJ, Skoggard S, Erkmann JA, Whitfield ML, Marzluff WF, Clarke HJ (December 2002). "Stem-loop binding protein accumulates during oocyte maturation and is not cell-cycle-regulated in the early mouse embryo". J. Cell Sci. 115 (Pt 23): 4577–86. doi:10.1242/jcs.00132. PMID 12415002.
- Zheng L, Dominski Z, Yang XC, Elms P, Raska CS, Borchers CH, Marzluff WF (March 2003). "Phosphorylation of stem-loop binding protein (SLBP) on two threonines triggers degradation of SLBP, the sole cell cycle-regulated factor required for regulation of histone mRNA processing, at the end of S phase". Mol. Cell. Biol. 23 (5): 1590–601. doi:10.1128/MCB.23.5.1590-1601.2003. PMC . PMID 12588979.
- Koseoglu MM, Graves LM, Marzluff WF (July 2008). "Phosphorylation of threonine 61 by cyclin a/Cdk1 triggers degradation of stem-loop binding protein at the end of S phase". Mol. Cell. Biol. 28 (14): 4469–79. doi:10.1128/MCB.01416-07. PMC . PMID 18490441.
- Sànchez R, Marzluff WF (October 2002). "The stem-loop binding protein is required for efficient translation of histone mRNA in vivo and in vitro". Mol. Cell. Biol. 22 (20): 7093–104. doi:10.1128/mcb.22.20.7093-7104.2002. PMC . PMID 12242288.
- Zhao X, McKillop-Smith S, Müller B (December 2004). "The human histone gene expression regulator HBP/SLBP is required for histone and DNA synthesis, cell cycle progression and cell proliferation in mitotic cells". J. Cell Sci. 117 (Pt 25): 6043–51. doi:10.1242/jcs.01523. PMID 15546920.
- Erkmann JA, Wagner EJ, Dong J, Zhang Y, Kutay U, Marzluff WF (June 2005). "Nuclear import of the stem-loop binding protein and localization during the cell cycle". Mol. Biol. Cell. 16 (6): 2960–71. doi:10.1091/mbc.E04-11-1023. PMC . PMID 15829567.
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.
Histone RNA hairpin-binding protein RNA-binding domain Provide feedback
This family represents the RNA-binding domain of histone RNA hairpin-binding protein .
Wang ZF, Whitfield ML, Ingledue TC 3rd, Dominski Z, Marzluff WF;, Genes Dev. 1996;10:3028-3040.: The protein that binds the 3' end of histone mRNA: a novel RNA-binding protein required for histone pre-mRNA processing. PUBMED:8957003 EPMC:8957003
This tab holds annotation information from the InterPro database.
InterPro entry IPR029344
This entry represents the RNA-binding domain of histone RNA hairpin-binding protein, also known as SLBP [PUBMED:8957003]. Proteins containing this domain include SLBP1 and SLBP2 from Xenopus laevis.
SLBP1 binds the 5' side of the stem-loop structure of replication-dependent histone pre-mRNAs and contributes to efficient 3'-end processing by stabilising the complex between histone pre-mRNA and U7 small nuclear ribonucleoprotein (snRNP), via the histone downstream element (HDE) [PUBMED:11157774]. It plays an important role in targeting mature histone mRNA from the nucleus to the cytoplasm and to the translation machinery. It stabilises mature histone mRNA and could be involved in cell-cycle regulation of histone gene expression [PUBMED:18036581, PUBMED:19470752, PUBMED:12588979, PUBMED:19155325].
SLBP2 binds to translationally inactive histone mRNA stored in immature oocytes. When oocytes mature, SLBP2 is degraded and a larger fraction of the histone mRNA is bound to SLBP1. Instead of having a role in histone pre-mRNA processing, SLBP2 may be a specific translational repressor [PUBMED:9858606].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||RNA binding (GO:0003723)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
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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...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
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You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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...
If you find these logos useful in your own work, please consider citing the following article:
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.
|Author:||Eberhardt RY, Coggill P, Hetherington K|
|Number in seed:||75|
|Number in full:||529|
|Average length of the domain:||68.90 aa|
|Average identity of full alignment:||46 %|
|Average coverage of the sequence by the domain:||17.58 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||5|
|Download:||download the raw HMM for this family|
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- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 SLBP_RNA_bind 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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