Summary: Bcr-Abl oncoprotein oligomerisation domain

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BCR gene Edit Wikipedia article

Breakpoint cluster region

PDB rendering based on 1k1f.

Available structures

PDB

Ortholog search: PDBe, RCSB

List of PDB id codes
1K1F, 2AIN

Identifiers

Symbols

BCR; ALL; BCR1; CML; D22S11; D22S662; PHL

External IDs

OMIM: 151410 MGI: 88141 HomoloGene: 3192 ChEMBL: 5146 GeneCards: BCR Gene

EC number

2.7.11.1

Gene Ontology
Molecular function	â¢ protein serine/threonine kinase activity â¢ protein tyrosine kinase activity â¢ Rho guanyl-nucleotide exchange factor activity â¢ GTPase activator activity â¢ protein binding â¢ ATP binding â¢ phospholipid binding â¢ kinase activity
Cellular component	â¢ cytosol
Biological process	â¢ protein phosphorylation â¢ signal transduction â¢ small GTPase mediated signal transduction â¢ regulation of Rho protein signal transduction â¢ positive regulation of GTPase activity â¢ regulation of small GTPase mediated signal transduction
Sources: Amigo / QuickGO

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 22:
23.52 â 23.66 Mb

Chr 10:
75.06 â 75.18 Mb

PubMed search

[1]

[2]

Bcr-Abl oncoprotein oligomerisation domain

structure of the bcr-abl oncoprotein oligomerization domain

Identifiers

Symbol

Bcr-Abl_Oligo

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

The breakpoint cluster region protein (BCR) also known as renal carcinoma antigen NY-REN-26 is a protein that in humans is encoded by the BCR gene. BCR is one of the two genes in the BCR-ABL complex, which is associated with the Philadelphia chromosome. Two transcript variants encoding different isoforms have been found for this gene.

[edit] Function

Although the BCR-ABL fusion protein has been extensively studied, the function of the normal BCR gene product is not clear. The protein has serine/threonine kinase activity and is a GTPase-activating protein for RAC1 and CDC42.^[1]

[edit] Clinical significance

A reciprocal translocation between chromosomes 22 and 9 produces the Philadelphia chromosome, which is often found in patients with chronic myelogenous leukemia. The chromosome 22 breakpoint for this translocation is located within the BCR gene. The translocation produces a fusion protein that is encoded by sequence from both BCR and ABL, the gene at the chromosome 9 breakpoint.^[2]

[edit] Structure

The Bcr-Abl oncoprotein oligomerisation domain found at the N-terminus of BCR is essential for the oncogenicity of the BCR-ABL fusion protein. The Bcr-Abl oncoprotein oligomerisation domain consists of a short N-terminal helix (alpha-1), a flexible loop and a long C-terminal helix (alpha-2). Together these form an N-shaped structure, with the loop allowing the two helices to assume a parallel orientation. The monomeric domains associate into a dimer through the formation of an antiparallel coiled coil between the alpha-2 helices and domain swapping of two alpha-1 helices, where one alpha-1 helix swings back and packs against the alpha-2 helix from the second monomer. Two dimers then associate into a tetramer.^[3]

[edit] Interactions

BCR gene has been shown to interact with:

Abl gene,^[4]^[5]^[6]
CD117,^[7]
CRKL^[8]^[9]^[10]^[11]
FES,^[12]^[13]
Grb2,^[13]^[8]^[14]^[9]^[4]^[15]
GRB10,^[8]
HCK,^[16]^[17]
MLLT4,^[18]
PXN,^[19]^[20]
PIK3CG,^[8]^[19]^[21]
PTPN6,^[22]
SOS1,^[13]^[4] and
XPB.^[23]

[edit] See also

Abl gene

[edit] References

^ "Entrez Gene: Breakpoint cluster region". http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=retrieve&list_uids=613.
^ "Entrez Gene: BCR breakpoint cluster region". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=613.
^ Zhao X, Ghaffari S, Lodish H, Malashkevich VN, Kim PS (February 2002). "Structure of the Bcr-Abl oncoprotein oligomerization domain". Nat. Struct. Biol. 9 (2): 117â20. doi:10.1038/nsb747. PMID 11780146.
^ ^a ^b ^c Puil L, Liu J, Gish G, Mbamalu G, Bowtell D, Pelicci P G, Arlinghaus R, Pawson T (February 1994). "Bcr-Abl oncoproteins bind directly to activators of the Ras signalling pathway". EMBO J. 13 (4): 764â73. PMC 394874. PMID 8112292. //www.ncbi.nlm.nih.gov/pmc/articles/PMC394874/.
^ Ling X, Ma Guozhen, Sun Tong, Liu Jiaxin, Arlinghaus Ralph B (January 2003). "Bcr and Abl interaction: oncogenic activation of c-Abl by sequestering Bcr". Cancer Res. 63 (2): 298â303. PMID 12543778.
^ Pendergast AM, Muller A J, Havlik M H, Maru Y, Witte O N (July 1991). "BCR sequences essential for transformation by the BCR-ABL oncogene bind to the ABL SH2 regulatory domain in a non-phosphotyrosine-dependent manner". Cell 66 (1): 161â71. doi:10.1016/0092-8674(91)90148-R. PMID 1712671.
^ Hallek M, Danhauser-Riedl S, Herbst R, Warmuth M, Winkler A, Kolb H J, Druker B, Griffin J D, Emmerich B, Ullrich A (July 1996). "Interaction of the receptor tyrosine kinase p145c-kit with the p210bcr/abl kinase in myeloid cells". Br. J. Haematol. 94 (1): 5â16. doi:10.1046/j.1365-2141.1996.6102053.x. PMID 8757502.
^ ^a ^b ^c ^d Bai RY, Jahn T, Schrem S, Munzert G, Weidner K M, Wang J Y, Duyster J (August 1998). "The SH2-containing adapter protein GRB10 interacts with BCR-ABL". Oncogene 17 (8): 941â8. doi:10.1038/sj.onc.1202024. PMID 9747873.
^ ^a ^b Million RP, Harakawa Nari, Roumiantsev Sergei, Varticovski Lyuba, Van Etten Richard A (June 2004). "A Direct Binding Site for Grb2 Contributes to Transformation and Leukemogenesis by the Tel-Abl (ETV6-Abl) Tyrosine Kinase". Mol. Cell. Biol. 24 (11): 4685â95. doi:10.1128/MCB.24.11.4685-4695.2004. PMC 416425. PMID 15143164. //www.ncbi.nlm.nih.gov/pmc/articles/PMC416425/.
^ Heaney C, Kolibaba K, Bhat A, Oda T, Ohno S, Fanning S, Druker B J (January 1997). "Direct binding of CRKL to BCR-ABL is not required for BCR-ABL transformation". Blood 89 (1): 297â306. PMID 8978305.
^ Kolibaba KS, Bhat A, Heaney C, Oda T, Druker B J (March 1999). "CRKL binding to BCR-ABL and BCR-ABL transformation". Leuk. Lymphoma 33 (1â2): 119â26. doi:10.3109/10428199909093732. PMID 10194128.
^ Lionberger JM, Smithgall T E (February 2000). "The c-Fes protein-tyrosine kinase suppresses cytokine-independent outgrowth of myeloid leukemia cells induced by Bcr-Abl". Cancer Res. 60 (4): 1097â103. PMID 10706130.
^ ^a ^b ^c Maru Y, Peters K L, Afar D E, Shibuya M, Witte O N, Smithgall T E (February 1995). "Tyrosine phosphorylation of BCR by FPS/FES protein-tyrosine kinases induces association of BCR with GRB-2/SOS". Mol. Cell. Biol. 15 (2): 835â42. PMC 231961. PMID 7529874. //www.ncbi.nlm.nih.gov/pmc/articles/PMC231961/.
^ Million RP, Van Etten R A (July 2000). "The Grb2 binding site is required for the induction of chronic myeloid leukemia-like disease in mice by the Bcr/Abl tyrosine kinase". Blood 96 (2): 664â70. PMID 10887132.
^ Ma G, Lu D, Wu Y, Liu J, Arlinghaus R B (May. 1997). "Bcr phosphorylated on tyrosine 177 binds Grb2". Oncogene 14 (19): 2367â72. doi:10.1038/sj.onc.1201053. PMID 9178913.
^ Stanglmaier M, Warmuth M, Kleinlein I, Reis S, Hallek M (February 2003). "The interaction of the Bcr-Abl tyrosine kinase with the Src kinase Hck is mediated by multiple binding domains". Leukemia 17 (2): 283â9. doi:10.1038/sj.leu.2402778. PMID 12592324.
^ Lionberger JM, Wilson M B, Smithgall T E (June 2000). "Transformation of myeloid leukemia cells to cytokine independence by Bcr-Abl is suppressed by kinase-defective Hck". J. Biol. Chem. 275 (24): 18581â5. doi:10.1074/jbc.C000126200. PMID 10849448.
^ Radziwill G, Erdmann R A, Margelisch U, Moelling K (July 2003). "The Bcr Kinase Downregulates Ras Signaling by Phosphorylating AF-6 and Binding to Its PDZ Domain". Mol. Cell. Biol. 23 (13): 4663â72. doi:10.1128/MCB.23.13.4663-4672.2003. PMC 164848. PMID 12808105. //www.ncbi.nlm.nih.gov/pmc/articles/PMC164848/.
^ ^a ^b Salgia R, Sattler M, Pisick E, Li J L, Griffin J D (February 1996). "p210BCR/ABL induces formation of complexes containing focal adhesion proteins and the protooncogene product p120c-Cbl". Exp. Hematol. 24 (2): 310â3. PMID 8641358.
^ Salgia R, Li J L, Lo S H, Brunkhorst B, Kansas G S, Sobhany E S, Sun Y, Pisick E, Hallek M, Ernst T (March 1995). "Molecular cloning of human paxillin, a focal adhesion protein phosphorylated by P210BCR/ABL". J. Biol. Chem. 270 (10): 5039â47. doi:10.1074/jbc.270.10.5039. PMID 7534286.
^ Skorski T, Kanakaraj P, Nieborowska-Skorska M, Ratajczak M Z, Wen S C, Zon G, Gewirtz A M, Perussia B, Calabretta B (July 1995). "Phosphatidylinositol-3 kinase activity is regulated by BCR/ABL and is required for the growth of Philadelphia chromosome-positive cells". Blood 86 (2): 726â36. PMID 7606002.
^ Liedtke M, Pandey P, Kumar S, Kharbanda S, Kufe D (October 1998). "Regulation of Bcr-Abl-induced SAP kinase activity and transformation by the SHPTP1 protein tyrosine phosphatase". Oncogene 17 (15): 1889â92. doi:10.1038/sj.onc.1202117. PMID 9788431.
^ Takeda N, Shibuya M, Maru Y (January 1999). "The BCR-ABL oncoprotein potentially interacts with the xeroderma pigmentosum group B protein". PNAS 96 (1): 203â7. doi:10.1073/pnas.96.1.203. PMC 15117. PMID 9874796. //www.ncbi.nlm.nih.gov/pmc/articles/PMC15117/.

[edit] Further reading

Wang L, Seale J, Woodcock BE, Clark RE (2002). "e19a2-positive chronic myeloid leukaemia with BCR exon e16-deleted transcripts". Leukemia 16 (8): 1562â3. doi:10.1038/sj.leu.2402600. PMID 12145699.

[edit] External links

BCR+protein,+human at the US National Library of Medicine Medical Subject Headings (MeSH)

PDB gallery

1k1f: Structure of the Bcr-Abl Oncoprotein Oligomerization domain

This article incorporates text from the public domain Pfam and InterPro IPR015123

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Bcr-Abl oncoprotein oligomerisation domain Provide feedback

The Bcr-Abl oncoprotein oligomerisation domain consists of a short N-terminal helix (alpha-1), a flexible loop and a long C-terminal helix (alpha-2). Together these form an N-shaped structure, with the loop allowing the two helices to assume a parallel orientation. The monomeric domains associate into a dimer through the formation of an antiparallel coiled coil between the alpha-2 helices and domain swapping of two alpha-1 helices, where one alpha-1 helix swings back and packs against the alpha-2 helix from the second monomer. Two dimers then associate into a tetramer. The oligomerisation domain is essential for the oncogenicity of the Bcr-Abl protein [1].

Literature references

Zhao X, Ghaffari S, Lodish H, Malashkevich VN, Kim PS; , Nat Struct Biol. 2002;9:117-120.: Structure of the Bcr-Abl oncoprotein oligomerization domain. PUBMED:11780146 EPMC:11780146

External database links

PANDIT:	PF09036
Pseudofam:	PF09036
SYSTERS:	Bcr-Abl_Oligo

This tab holds annotation information from the InterPro database.

InterPro entry IPR015123

This entry represents the oligomerisation domain of the breakpoint cluster region oncoprotein Bcr, and the Bcr/Abl (Abelson-leukemia-virus) fusion protein created by a reciprocal (9;22) fusion [PUBMED:17090304]. Brc displays serine/threonine protein kinase activity (EC), acting as a GTPase-activating protein for RAC1 and CDC42. Brc promotes the exchange of RAC or CDC42-bound GDP by GTP, thereby activating them [PUBMED:15302586]. The Bcr/Abl fusion protein loses some of the regulatory function of Bcr with regards to small Rho-like GTPases with negative consequences on cell motility, in particular on the capacity to adhere to endothelial cells [PUBMED:17090304].

The Bcr, Bcr/Abl oncoprotein oligomerisation domain consists of a short N-terminal helix (alpha-1), a flexible loop and a long C-terminal helix (alpha-2). Together these form an N-shaped structure, with the loop allowing the two helices to assume a parallel orientation. The monomeric domains associate into a dimer through the formation of an antiparallel coiled coil between the alpha-2 helices and domain swapping of two alpha-1 helices, where one alpha-1 helix swings back and packs against the alpha-2 helix from the second monomer. Two dimers then associate into a tetramer. The oligomerisation domain is essential for the oncogenicity of the Bcr-Abl protein [PUBMED:11780146].

Gene Ontology

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

Molecular function	protein serine/threonine kinase activity (GO:0004674)
	GTPase activator activity (GO:0005096)
Biological process	signal transduction (GO:0007165)
	protein phosphorylation (GO:0006468)

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

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Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

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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.

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 (4)	Full (67)	Representative proteomes				NCBI (63)	Meta (0)
	Seed (4)	Full (67)	RP15 (2)	RP35 (5)	RP55 (15)	RP75 (23)	NCBI (63)	Meta (0)
Jalview	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 (4)	Full (67)	Representative proteomes				NCBI (63)	Meta (0)
	Seed (4)	Full (67)	RP15 (2)	RP35 (5)	RP55 (15)	RP75 (23)	NCBI (63)	Meta (0)
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 (4)	Full (67)	Representative proteomes				NCBI (63)	Meta (0)
	Seed (4)	Full (67)	RP15 (2)	RP35 (5)	RP55 (15)	RP75 (23)	NCBI (63)	Meta (0)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	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.

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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:

pdb_1k1f

Previous IDs:

none

Type:

Domain

Author:

Mistry J, Sammut SJ

Number in seed:

4

Number in full:

67

Average length of the domain:

72.20 aa

Average identity of full alignment:

81 %

Average coverage of the sequence by the domain:

8.04 %

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	20.9	20.9
Trusted cut-off	21.1	32.0
Noise cut-off	20.4	19.0

Model length:

79

Family (HMM) version:

5

Download:

download the raw HMM for this family

Species distribution

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How the sunburst is generated

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phylum
class
order
family
genus
species

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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.

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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.

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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 Bcr-Abl_Oligo 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 seqence.

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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Bcr-Abl_Oligo (PF09036)

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