Summary: BOP1NT (NUC169) domain

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Wikipedia: BOP1
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This is the Wikipedia entry entitled "BOP1". More...

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BOP1 Edit Wikipedia article

Block of proliferation 1

Identifiers

Symbols

BOP1; KIAA0124

External IDs

OMIM: 610596 MGI: 1334460 HomoloGene: 6612 GeneCards: BOP1 Gene

Gene Ontology
Molecular function	• protein binding
Cellular component	• nucleoplasm • ribonucleoprotein complex • PeBoW complex
Biological process	• maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) • cell proliferation • ribosome biogenesis • regulation of cell cycle
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 8:
145.49 – 145.52 Mb

Chr 15:
76.45 – 76.48 Mb

PubMed search

[1]

[2]

BOP1NT

Identifiers

Symbol

BOP1NT

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Ribosome biogenesis protein BOP1 is a protein that in humans is encoded by the BOP1 gene.^[1]^[2] It is a WD40 repeat-containing nucleolar protein involved in rRNA processing, thereby controlling the cell cycle.^[3] It is required for the maturation of the 25S and 5.8S ribosomal RNAs. It may serve as an essential factor in ribosome formation that coordinates processing of the spacer regions in pre-rRNA. The Pes1-Bop1 complex has several components: BOP1, GRWD1, PES1, ORC6L, and RPL3 and is involved in ribosome biogenesis and altered chromosome segregation. The overexpression of BOP1 increases the percentage of multipolar spindles in human cells. Deregulation of the BOP1 pathway may contribute to colorectal tumourigenesis in humans.^[4] Elevated levels of Bop1 induces Bop1/WDR12 and Bop1/Pes1 subcomplexes and the assembly and integrity of the PeBoW complex is highly sensitive to changes in Bop1 protein levels.^[5]

Nop7p-Erb1p-Ytm1p, found in yeast, is potentially the homologous complex of Pes1-Bop1-WDR12 as it is involved in the control of ribosome biogenesis and S phase entry. The integrity of the PeBoW complex is required for ribosome biogenesis and cell proliferation in mammalian cells.^[6] In Giardia, the species specific cytoskeleton protein, beta-giardin, interacts with Bop1.^[3]

BOP1 contains a conserved N-terminal domain, BOP1NT.

[edit] References

^ Nagase T, Seki N, Tanaka A, Ishikawa K, Nomura N (Mar 1996). "Prediction of the coding sequences of unidentified human genes. IV. The coding sequences of 40 new genes (KIAA0121-KIAA0160) deduced by analysis of cDNA clones from human cell line KG-1". DNA Res 2 (4): 167–74, 199–210. doi:10.1093/dnares/2.4.167. PMID 8590280.
^ "Entrez Gene: BOP1 block of proliferation 1". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=23246.
^ ^a ^b Kim J, Goo SY, Chung HJ, Yang HW, Yong TS, Lee KH, Park SJ (January 2006). "Interaction of beta-giardin with the Bop1 protein in Giardia lamblia". Parasitol. Res. 98 (2): 138â44. doi:10.1007/s00436-005-0040-8. PMID 16362343.
^ Killian A, Sarafan-Vasseur N, Sesboue R, Le Pessot F, Blanchard F, Lamy A, Laurent M, Flaman JM, Frebourg T (September 2006). "Contribution of the BOP1 gene, located on 8q24, to colorectal tumorigenesis". Genes Chromosomes Cancer 45 (9): 874â81. doi:10.1002/gcc.20351. PMID 16804918.
^ Rohrmoser M, Holzel M, Grimm T, Malamoussi A, Harasim T, Orban M, Pfisterer I, Gruber-Eber A, Kremmer E, Eick D (May 2007). "Interdependence of Pes1, Bop1, and WDR12 controls nucleolar localization and assembly of the PeBoW complex required for maturation of the 60S ribosomal subunit". Mol. Cell. Biol. 27 (10): 3682â94. doi:10.1128/MCB.00172-07. PMC 1899993. PMID 17353269. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1899993/.
^ Holzel M, Rohrmoser M, Schlee M, Grimm T, Harasim T, Malamoussi A, Gruber-Eber A, Kremmer E, Hiddemann W, Bornkamm GW, Eick D (August 2005). "Mammalian WDR12 is a novel member of the Pes1-Bop1 complex and is required for ribosome biogenesis and cell proliferation". J. Cell Biol. 170 (3): 367â78. doi:10.1083/jcb.200501141. PMC 2171466. PMID 16043514. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2171466/.

[edit] Further reading

Zhang Y, Koushik S, Dai R, Mivechi NF (1999). "Structural organization and promoter analysis of murine heat shock transcription factor-1 gene.". J. Biol. Chem. 273 (49): 32514–21. doi:10.1074/jbc.273.49.32514. PMID 9829985.
Nakatsura T, Senju S, Yamada K, et al. (2001). "Gene cloning of immunogenic antigens overexpressed in pancreatic cancer.". Biochem. Biophys. Res. Commun. 281 (4): 936–44. doi:10.1006/bbrc.2001.4377. PMID 11237751.
Pestov DG, Strezoska Z, Lau LF (2001). "Evidence of p53-dependent cross-talk between ribosome biogenesis and the cell cycle: effects of nucleolar protein Bop1 on G(1)/S transition.". Mol. Cell. Biol. 21 (13): 4246–55. doi:10.1128/MCB.21.13.4246-4255.2001. PMC 87085. PMID 11390653. //www.ncbi.nlm.nih.gov/pmc/articles/PMC87085/.
Pestov DG, Stockelman MG, Strezoska Z, Lau LF (2001). "ERB1, the yeast homolog of mammalian Bop1, is an essential gene required for maturation of the 25S and 5.8S ribosomal RNAs.". Nucleic Acids Res. 29 (17): 3621–30. doi:10.1093/nar/29.17.3621. PMC 55883. PMID 11522832. //www.ncbi.nlm.nih.gov/pmc/articles/PMC55883/.
Andersen JS, Lyon CE, Fox AH, et al. (2002). "Directed proteomic analysis of the human nucleolus.". Curr. Biol. 12 (1): 1–11. doi:10.1016/S0960-9822(01)00650-9. PMID 11790298.
Strezoska Z, Pestov DG, Lau LF (2002). "Functional inactivation of the mouse nucleolar protein Bop1 inhibits multiple steps in pre-rRNA processing and blocks cell cycle progression.". J. Biol. Chem. 277 (33): 29617–25. doi:10.1074/jbc.M204381200. PMID 12048210.
Scherl A, Couté Y, Déon C, et al. (2003). "Functional proteomic analysis of human nucleolus.". Mol. Biol. Cell 13 (11): 4100–9. doi:10.1091/mbc.E02-05-0271. PMC 133617. PMID 12429849. //www.ncbi.nlm.nih.gov/pmc/articles/PMC133617/.
Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932. //www.ncbi.nlm.nih.gov/pmc/articles/PMC139241/.
Lapik YR, Fernandes CJ, Lau LF, Pestov DG (2004). "Physical and functional interaction between Pes1 and Bop1 in mammalian ribosome biogenesis.". Mol. Cell 15 (1): 17–29. doi:10.1016/j.molcel.2004.05.020. PMID 15225545.
Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).". Genome Res. 14 (10B): 2121–7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334. //www.ncbi.nlm.nih.gov/pmc/articles/PMC528928/.
Andersen JS, Lam YW, Leung AK, et al. (2005). "Nucleolar proteome dynamics.". Nature 433 (7021): 77–83. doi:10.1038/nature03207. PMID 15635413.
Nousiainen M, Silljé HH, Sauer G, et al. (2006). "Phosphoproteome analysis of the human mitotic spindle.". Proc. Natl. Acad. Sci. U.S.A. 103 (14): 5391–6. doi:10.1073/pnas.0507066103. PMC 1459365. PMID 16565220. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1459365/.
Beausoleil SA, Villén J, Gerber SA, et al. (2006). "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.". Nat. Biotechnol. 24 (10): 1285–92. doi:10.1038/nbt1240. PMID 16964243.
Olsen JV, Blagoev B, Gnad F, et al. (2006). "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.". Cell 127 (3): 635–48. doi:10.1016/j.cell.2006.09.026. PMID 17081983.
Ewing RM, Chu P, Elisma F, et al. (2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry.". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/msb4100134. PMC 1847948. PMID 17353931. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1847948/.

This article incorporates text from the public domain Pfam and InterPro IPR012953

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BOP1NT (NUC169) domain Provide feedback

This N terminal domain is found in BOP1-like WD40 proteins [1].

Literature references

Staub E, Fiziev P, Rosenthal A, Hinzmann B; , Bioessays 2004;26:567-581.: Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire. PUBMED:15112237 EPMC:15112237

External database links

PANDIT:	PF08145
Pseudofam:	PF08145
SYSTERS:	BOP1NT

This tab holds annotation information from the InterPro database.

InterPro entry IPR012953

This domain is found in the N-terminal region of BOP1-like WD40 proteins. Bop1 is a nucleolar protein involved in rRNA processing, thereby controlling the cell cycle [PUBMED:16362343]. It is required for the maturation of the 25S and 5.8S ribosomal RNAs. It may serve as an essential factor in ribosome formation that coordinates processing of the spacer regions in pre-rRNA.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Biological process	regulation of cell cycle (GO:0051726)
	rRNA processing (GO:0006364)

Domain organisation

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

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Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

Selex
Stockholm
FASTA
MSF

You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

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.

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 (38)	Full (353)	Representative proteomes				NCBI (359)	Meta (9)
	Seed (38)	Full (353)	RP15 (96)	RP35 (148)	RP55 (210)	RP75 (249)	NCBI (359)	Meta (9)
Jalview	View	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (38)	Full (353)	Representative proteomes				NCBI (359)	Meta (9)
	Seed (38)	Full (353)	RP15 (96)	RP35 (148)	RP55 (210)	RP75 (249)	NCBI (359)	Meta (9)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

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 (38)	Full (353)	Representative proteomes				NCBI (359)	Meta (9)
	Seed (38)	Full (353)	RP15 (96)	RP35 (148)	RP55 (210)	RP75 (249)	NCBI (359)	Meta (9)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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'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:

Staub E

Previous IDs:

none

Type:

Domain

Author:

Staub E, Bateman A, Mistry J

Number in seed:

38

Number in full:

353

Average length of the domain:

244.50 aa

Average identity of full alignment:

45 %

Average coverage of the sequence by the domain:

35.02 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	25.0	25.0
Trusted cut-off	25.3	25.4
Noise cut-off	21.8	24.5

Model length:

260

Family (HMM) version:

7

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

Show

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...

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:

superkingdom
kingdom
phylum
class
order
family
genus
species

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".

Sub-species

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.

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Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Species trees

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.

Interactive tree

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
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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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.

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: BOP1NT (PF08145)

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