View source for DEPDC1B

{{Infobox_gene}}

'''DEP Domain Containing Protein 1B''' also known as '''XTP1''', '''XTP8''','''HBV XAg-Transactivated Protein 8''', [formerly referred to as [[BRCC3]]] is a human [[protein]] encoded by a [[gene]] of similar name located on  [[chromosome 5]].<ref>{{cite journal | last1 = Morimoto | first1 = K | year = 1996 | title = Characterization of a unique variant of bat rabies virus responsible for newly emerging human cases in North America | url = | journal = Proceedings of the National Academy of Sciences | volume = 93 | issue = 11| pages = 5653–5658 | doi = 10.1073/pnas.93.11.5653 | pmc = 39303 }}</ref><ref name="Entrez">Entrez Gene: DEPDC1B https://www.ncbi.nlm.nih.gov/gene?LinkName=protein_gene&from_uid=223633999</ref><ref>Gene Cards: DEPDC1B  https://www.genecards.org/cgi-bin/carddisp.pl?gene=DEPDC1B</ref>

The precise function of DEPDC1B is currently unknown. Expression profiles indicate that DEPDC1B is highly expressed ubiquitously throughout human tissue.<ref name="GEO">NCBI GEO https://www.ncbi.nlm.nih.gov/geoprofiles</ref>

==Gene structure==

===Gene neighborhood===

[[File:DEPDC1B Gene Locus - Chromosome 5.png|thumb|300px| left|DEPDC1B gene locus]]														

DEPDC1B is found on the long arm of chromosome 5 (5q12.1), spanning 103kb on the minus strand. The gene neighborhood of DEPDC1B includes 5 other genes. Downstream are two genes [[SEPT21]] and [[PDE4D]]. Upstream are another two genes [[ELOV7]] and [[KRT8P31]]. On the complement strand is another gene in the same region [[PART1]].<ref name=Entrez />

===Promoter===

DEPDC1B promoter region contains several transcription factors associated with proteins of ubiquitous expression. These transcription factors possess a central theme of cellular proliferation, cell cycle regulation, apoptosis, and differentiation. Few promoters unique to tumor suppression or tumorgenesis exist within the region as well.<ref>Genomatix Software. "Genomatix ElDorado". Retrieved 1998-2014.</ref>
 
The following includes the top twenty Predicted Transcription Factors:

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{{ordered list|start=1|[[CREB]] cAMP-responsive element binding proteins|[[NRF1]] nuclear respiratory factor 1|[[CCAAT-enhancer-binding proteins]] factor|KRAB domain zinc finger protein 57| [[Interferon]] Regulatory Factors}}
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{{ordered list|start=6|Vertebrate caudal related homeodomain protein|C2H2 [[Zinc Finger Transcription Factor]]s 1|Human and Murine [[ETS1]] factors|Selenocysteine tRNA activating factor|GC-Box factors SP1/GC}}
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{{ordered list|start=11|C2H2 Zinc Finger Transcription Factors 2|PREB core-binding element|Activator-, mediator- and TBP-dependent core promoter element for RNA polymerase II transcription from TATA-less promoters|Cell cycle regulators: Cell cycle homology element|Core promoter motif ten elements}}
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{{ordered list|start=16|Human muscle-specific Mt binding site|PAX-2/5/8 binding sites|RNA polymerase II [[transcription factor II B]]|Cellular and viral myb-like transcriptional regulators|Abdominal-B type homeodomain transcription factors}}
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==mRNA structure==

===Splice variants===
[[File:DEPDC1B confirmed spice variants.png|thumb|450px|right|The two confirmed DEPDC1B mRNA splice variants]]
DEPDC1B possesses 13 mRNA splice variants that form two isoforms. Isoform 1 is the longest and is the most commonly used version of the gene. It is composed of 11 exons and is 103254bp in length. Isoform 2 is the second confirmed transcript variant. It is composed of 10 exons, missing the tenth exon of the first variant. The missing exon is 186bp in length.<ref>NCBI AceView https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&q=DEPDC1B</ref> See ''Protein Structure'' section for more detail...

===Secondary structure===
DEPDC1B is predicted to be predominantly alpha-helical. No significant beta-strands or beta structures exist with the protein.
.<ref>BPS : A. W. Burgess and P. K. Ponnuswamy and H. A. Sheraga, Analysis of conformations of amino acid residues and prediction of backbone topography in proteins, Israel J. Chem., p239-286, 1974, vol12.
D_R : G. Dele`age and B. Roux, An algorithm for secondary structure prediction based on class prediction, Protein Engineering, p289-294, 1987, vol 1, num 4.

DSC : Ross D. King and Michael J.E. Sternberg - Identification and application of the concepts important for accurate and reliable protein secondary structure prediction. ''Protein Science'', 1996, 5:2298-2310

GGR : Garnier, Gibrat, and Robson, Meth. Enzymol., R.F. Doolittle ed. 1996, 266:97-120

GOR : Jean Garnier and D. J. Osguthorpe and Barry Robson, Analysis of the accuracy and implications of simple methods for predicting the secondary structure of proteins, J. Mol. Biol., p 97-120, 1978, vol 120.

G_G : O. Gascuel and J. L. Golmard, A simple method for predicting the secondary structure of globular proteins: implications and accuracy, CABIOS, p 357-365, 1988, vol 4.

H_K : L. Howard Holley and Martin Karplus, Protein secondary structure prediction with a neural network, Proc. Natl. Acad. Sci. USA, p 152-156, Jan 1989, vol 86.

K_S : Ross D. King and Michael J. E. Sternberg, Machine learning approach for the prediction of protein secondary structure, J. Mol. Biol., p 441-457, 1990, vol 216.

L_G : Jonathan M. Levin and Jean Garnier, Improvements in a secondary structure prediction method based on a search for local sequence homologies and its use as a model building tool, Biochim. Biophys. Acta., p 283-295, 1988, vol 955.

Q_S : Ning Qian and Terence Sejnowski, Predicting the secondary structure of proteins using neural network models, J. Mol. Biol., p 865-884, 1988, vol 202.

JOI Joint prediction - Prediction made by the program that assigns the structure using a "winner takes all" procedure for each amino acid prediction using the other methods.</ref>

===Stem loops and binding miRNA===
DEPDC1B is predicted to possess multiple [[stem loops]] in its 5' and 3' untranslated regions (UTR)<ref>Mfold http://mfold.rna.albany.edu/</ref><ref>Sfold http://sfold.wadsworth.org/</ref>
. In the 3' UTR, miRNA ''has-miR-499-5p'' binds to a nucleotide region predicted as a stem loop.<ref>TragetScan http://www.targetscan.org/</ref>

==Protein structure==

===Sequence===

The DEPDC1B gene possesses two novel proteoforms. The longest variation, coded by mRNA isoform 1, is the most commonly used. The protein is 529 amino acids in length. The second novel proteoform, DEPDC1B.2 is coded by 10 exons, missing the 10th exon from the longest variation. The protein is 467 amino acids in length. The missing 62 amino acids follow the RhoGAP domain, in a region predicted to be highly phosphorylated<ref name="Uniprot">Q8WUY9 (DEP1B_HUMAN) https://www.uniprot.org/uniprot/Q8WUY9</ref>

===Domains===

[[File:Solution Structure - Human DEP Domain.png|thumb|left|Solution structure for the human DEP domain]]

DEPDC1B contains two structural domains: a [[DEP domain]] and a [[RhoGAP domain]].

The DEP domain is primarily found in proteins involved in [[G-protein]] [[signalling pathways]] and regulation of [[GTPase]].<ref>{{cite journal | vauthors = Burchett SA | title = Regulators of G protein signaling: a bestiary of modular protein binding domains | journal = Journal of Neurochemistry | volume = 75 | issue = 4 | pages = 1335–51 | date = October 2000 | pmid = 10987813 | doi = 10.1046/j.1471-4159.2000.0751335.x }}</ref><ref>{{cite journal | vauthors = Wong HC, Mao J, Nguyen JT, Srinivas S, Zhang W, Liu B, Li L, Wu D, Zheng J | title = Structural basis of the recognition of the dishevelled DEP domain in the Wnt signaling pathway | journal = Nature Structural Biology | volume = 7 | issue = 12 | pages = 1178–84 | date = December 2000 | pmid = 11101902 | doi = 10.1038/82047 | pmc = 4381838 }}</ref> As well, experimental evidence suggests that the DEP domain determines the subcellular target of some GTPase Activating proteins.<ref>{{cite journal | last1 = Martemyanov | first1 = K | display-authors = etal   | year = 2003 | title = The DEP Domain Determines Subcellular Targeting of the GTPase Activating Protein RGS9 In Vivo | url = | journal = The Journal of Neuroscience | volume = 23 | issue = 12| pages = 10175–10181 }}</ref> In the DEPDC1B protein electronic inference has verified the GTPase activator activity function.<ref name=Uniprot /> The solution structure of human containing DEP domain containing proteins verifies the secondary structure of the domain: containing three alpha-helices and two beta-strands within the approximate 80 amino acid region of the domain.<ref>Zhang HP, Hayashi F, Yokoyama S. (2007) Solution structure of the dep domain from human dep domain-containing protein 1. https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=2ysr</ref><ref name="pmid22135289">{{cite journal | vauthors = Madej T, Addess KJ, Fong JH, Geer LY, Geer RC, Lanczycki CJ, Liu C, Lu S, Marchler-Bauer A, Panchenko AR, Chen J, Thiessen PA, Wang Y, Zhang D, Bryant SH | title = MMDB: 3D structures and macromolecular interactions | journal = Nucleic Acids Research | volume = 40 | issue = Database issue | pages = D461–4 | year = 2012 | pmid = 22135289 | pmc = 3245041 | doi = 10.1093/nar/gkr1162 }}</ref>

The RhoGAP domain is another structural domain known to interact with GTPase and small GTPase. Research concerning the domain in other proteins indicates an approximately similar function among the domain in various proteins. The domain has been verified to interact with other proteins to form complexes or interact with other strcuutres of the cell such as the [[cytoskeleton]] or [[plasma membrane]].<ref>{{cite journal | vauthors = Peck J, Douglas G, Wu CH, Burbelo PD | title = Human RhoGAP domain-containing proteins: structure, function and evolutionary relationships | journal = FEBS Letters | volume = 528 | issue = 1-3 | pages = 27–34 | date = September 2002 | pmid = 12297274 | doi = 10.1016/s0014-5793(02)03331-8 }}</ref>

===Post-translational modification===
DEPDC1B protein product is predicted to be highly phosphorylated after translation.<ref>{{cite journal | vauthors = Blom N, Gammeltoft S, Brunak S | title = Sequence and structure-based prediction of eukaryotic protein phosphorylation sites | journal = Journal of Molecular Biology | volume = 294 | issue = 5 | pages = 1351–62 | date = December 1999 | pmid = 10600390 | doi = 10.1006/jmbi.1999.3310 }}</ref> A single sumolaytion site, found within the RhoGAP domain, indicates the possible interaction of the protein with a [[SUMO protein]], enabling or inhibiting interaction with other proteins.<ref>Expasy SumoSP http://sumosp.biocuckoo.org/</ref> A single palmitoylation site, found within the RhoGAP domain, indicates the possible interaction of the DEPDC1B protein product with a membrane via lipid anchor.<ref>Expasy CSS-Palm http://csspalm.biocuckoo.org/</ref>

No conserved glycolation sites are predicted within the mature DEPDC1B protein product.<ref>Prediction of N-glycosylation sites in human proteins. R. Gupta, E. Jung and S. Brunak. In preparation, 2004.</ref> No signal peptide or [[transmembrane domain]]s are predicted within human or any ortholog protein.<ref name="pmid12456873">{{cite journal | vauthors = Cserzö M, Eisenhaber F, Eisenhaber B, Simon I | title = On filtering false positive transmembrane protein predictions | journal = Protein Engineering | volume = 15 | issue = 9 | pages = 745–52 | year = 2002 | pmid = 12456873 | doi = }}</ref><ref>SignalP 4.0: discriminating signal peptides from transmembrane regions Thomas Nordahl Petersen, Søren Brunak, Gunnar von Heijne & Henrik Nielsen Nature Methods, 8:785-786, 2011 doi: 10.1038/nmeth.1701 {{PMID|21959131}}</ref> No prenylation sites are predicted in any DEPDC1B orthologs.<ref>Expasy PrePS http://mendel.imp.ac.at/sat/PrePS/index.html</ref>

===Expression===
[[File:DEPDC1B - Large-scale analysis of the mouse transcriptome.png|thumb|650px |right|Mouse DEPDC1B large-scale tissue expression]]
Expression of DEPDC1B is reported to be largely ubiquitous throughout mouse tissue. High level of gene expression is observed in all periods of life, except early zygote stages.<ref name=GEO /> Experimental evidence suggests that DEPDC1B presents similar ubiquitous expression in all tissues.<ref>BioGPS http://biogps.org/#goto=genereport&id=55789</ref>

Differential expression profiles suggest that DEPDC1B is higher expressed in many cancerous disease states, including: papillary thyroid cancer,<ref>NCBI GEO https://www.ncbi.nlm.nih.gov/geoprofiles/18885436</ref> breast cancer,<ref>NCBI GEO https://www.ncbi.nlm.nih.gov/geoprofiles/36185472M</ref> synovial sarcoma,<ref>NCBI GEO https://www.ncbi.nlm.nih.gov/geoprofiles/38187695</ref> and prostatic cancer progression.<ref>NCBI GEO https://www.ncbi.nlm.nih.gov/geoprofiles/14261636</ref> Also, DEPDC1B expression decreases in environments of beta-catenin depletion in multiple myeloma cell lines<ref>NCBI GEO https://www.ncbi.nlm.nih.gov/geoprofiles/61462636</ref>

=== Interactions ===

<!-- Deleted image removed: [[File:Predicted Protein Interaction of DEPDC1B.png|thumb|left|Predicted protein interactions of DEPDC1B]] -->
No interactions of DEPDC1B within any other protein product characterized by experimentation have been verified.<ref name="string">String http://string-db.org/newstring_cgi/show_network_section.pl</ref>

Medium coexpression of DEPDC1B with [[ECT2]] in cell cycle regulation and DNA synthesis was verified by similarity of expression in various tissues.<ref name=string /> The remaining predicted interaction were determined via datamining.

==Homology==

===Orthologs===
DEPDC1B is unique to [[Chordates]] in Kingdom [[Animalia]]<ref name="BLAST">NCBI BLAST http://blast.ncbi.nlm.nih.gov/Blast.cgi</ref>

Multiple sequence alignments verify that DEPDC1B is highly conserved among orthologs.<ref>{{cite journal | vauthors = Higgins DG, Bleasby AJ, Fuchs R | title = CLUSTAL V: improved software for multiple sequence alignment | journal = Computer Applications in the Biosciences | volume = 8 | issue = 2 | pages = 189–91 | date = April 1992 | pmid = 1591615 | doi = 10.1093/bioinformatics/8.2.189 }}</ref><ref>{{cite journal | vauthors = Thompson JD, Higgins DG, Gibson TJ | title = CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice | journal = Nucleic Acids Research | volume = 22 | issue = 22 | pages = 4673–80 | date = November 1994 | pmid = 7984417 | pmc = 308517 | doi = 10.1093/nar/22.22.4673 }}</ref><ref>{{cite journal | last1 = Felsenstein | first1 = J | year = 1989 | title = PHYLIP -- Phylogeny Inference Package (Version 3.2) | doi = 10.1111/j.1096-0031.1989.tb00562.x | journal = Cladistics | volume = 5 | issue = | pages = 164–166 }}</ref><ref>CLUSTAL W: Julie D. Thompson, Desmond G. Higgins and Toby J. Gibson, modified; any errors are due to the modifications. PHYLIP: Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.</ref>
The two structural domains (DEP and RhoGAP) are the two most conserved elements of the proteins. Various motifs are also conserved throughout the protein. No data suggesting motif function could be determined. All predicted post-translational modification were confirmed to be conserved in the orthologous proteins.

DEPDC1B evolution is predicted to follow the general species evolution.
{| border="5" align="center" style="text-align:center" cellpadding="5" cellspacing="0"
|+'''DEPDC1B Orthologs'''
! scope="col" width="150px" style="background: #ffdead;" | Genus and species
! scope="col" width="150px" style="background: #efefef;" | Common name 
! scope="col" width="100px" style="background: #ffdead;"  | Class   
! scope="col" width="150px" style="background: #efefef;" | Divergence (mya)<ref>{{cite journal | vauthors = Hedges SB, Dudley J, Kumar S | title = TimeTree: a public knowledge-base of divergence times among organisms | journal = Bioinformatics | volume = 22 | issue = 23 | pages = 2971–2 | date = December 2006 | pmid = 17021158 | doi = 10.1093/bioinformatics/btl505 }}</ref>
! scope="col" width="200px" style="background: #ffdead;" | Accession 
! scope="col" width="150px" style="background: #efefef;" | Percent Identity<ref name=BLAST />
|-
| ''Nomascus leucogenys'' || [[Northern white-cheeked gibbon]] || [[Mammalia]] || 20.4 || XP_003266016 [https://www.ncbi.nlm.nih.gov/protein/XP_003266016/] || 98%
|- 
| ''Papio anubis '' || [[Olive baboon]] || Mammalia  || 29 || XP_003899752 [https://www.ncbi.nlm.nih.gov/protein/XP_003899752/] || 98%
|- 
| ''Mus musculus'' || [[House mouse]] || Mammalia || 92.3 || NP_848798 [https://www.ncbi.nlm.nih.gov/protein/NP_848798/] || 94%
|-
| ''Pteropus alecto'' || [[Black flying fox]] || Mammalia || 94.2 || XP_006906108 [https://www.ncbi.nlm.nih.gov/protein/XP_006906108/] || 96%
|-
| ''Felis catus'' || [[Domestic cat]] || Mammalia || 94.2 || XP_003981045 [https://www.ncbi.nlm.nih.gov/protein/XP_003981045/] || 96%
|-
| ''Bos taurus'' || [[Cow]] || Mammalia || 94.2 || XP_005221558 [https://www.ncbi.nlm.nih.gov/protein/XP_005221558/] || 95%
|-
| ''Monodelphis domestica'' || [[Gray short-tailed opossum]] || Mammalia || 162.6 || XP_001363879 [https://www.ncbi.nlm.nih.gov/protein/XP_001363879/] || 88%
|-
| ''Ficedula albicollis'' || [[Collared flycatcher]] || [[Ave]] || 296 || XP_005060715 [https://www.ncbi.nlm.nih.gov/protein/XP_005060715/] || 77%
|-
| ''Taeniopygia guttata'' || [[Zebra finch]] || Ave || 296 || XP_002188294 [https://www.ncbi.nlm.nih.gov/protein/XP_002188294/] || 76%
|-
| ''Gallus gallus '' || [[Chicken]] || Ave || 296 || NP_001006576 [https://www.ncbi.nlm.nih.gov/protein/NP_001006576/] || 75%
|-
| ''Anolis carolinensis'' || [[Green anole]] || [[Reptilia]] || 296 || XP_003216290 [https://www.ncbi.nlm.nih.gov/protein/XP_003216290/] || 76%
|-
| ''Xenopus tropicalis'' || [[Western clawed frog]] || [[Amphibia]] || 371.2 || NP_001121488 [https://www.ncbi.nlm.nih.gov/protein/NP_001121488/] || 68%
|-
| ''Lepisosteus oculatus '' || [[Spotted gar]] || [[Actinopterygii]] || 400.1 || XP_006626875 [https://www.ncbi.nlm.nih.gov/protein/XP_006626875/] || 68%
|-
| ''Maylandia zebra'' || [[Zebra mbuna]] || Actinopterygii || 400.1 || XP_004566850 [https://www.ncbi.nlm.nih.gov/protein/XP_004566850/] || 57%
|}

===Paralogs===
[[File:Evolutionary History of DEPDC1B with Paralogs (DEPDC1A and DEPDC7).gif|thumb|300px|right|Evolutionary relationship of DEPDC1B to paralogs - DEPDC1A and DEPDC7]]
DEPDC1B possesses two significant paralogs - [[DEPDC1A]] and [[DEPDC7]]

Multiple sequence alignment and phylogenetic analysis indicates DEPDC1A as the most recent paralog, diverging approximately 600 million years ago. DEPDC1A has been researched in several disease states.  High expression of the protein in Multiple Myeloma (MM) malignant plasma cells is associated with patient fatality. The high expression has been confirmed using conditional lentiviral vector delivery “to inhibit growth of human melanoma cell lines (HMCLs), with a block in G2 phase of the cell cycle, p53 phosphorylation and stabilization, and p21Cip1 accumulation”9.<ref name="pmid23646139">{{cite journal | vauthors = Kassambara A, Schoenhals M, Moreaux J, Veyrune JL, Rème T, Goldschmidt H, Hose D, Klein B | title = Inhibition of DEPDC1A, a bad prognostic marker in multiple myeloma, delays growth and induces mature plasma cell markers in malignant plasma cells | journal = PLoS One | volume = 8 | issue = 4 | pages = e62752 | year = 2013 | pmid = 23646139 | pmc = 3640027 | doi = 10.1371/journal.pone.0062752 }}</ref> In the same study it was concluded that DEPDC1A may contribute to the plasmablast features of MM cells, blocking differentiation. Study of DEPDC1A in bladder carcinogenesis revealed the gene as a possible antigen for the formation of bladder cancer cells. Using microarray and northern blotting confirmed the presence of unsubstantial amounts of the protein within the normal tissues, excluding the testis. Currently the gene is a potential target molecule for therapeutic treatment of bladder carcinogenesis.<ref>{{cite journal | vauthors = Kanehira M, Harada Y, Takata R, Shuin T, Miki T, Fujioka T, Nakamura Y, Katagiri T | title = Involvement of upregulation of DEPDC1 (DEP domain containing 1) in bladder carcinogenesis | journal = Oncogene | volume = 26 | issue = 44 | pages = 6448–55 | date = September 2007 | pmid = 17452976 | doi = 10.1038/sj.onc.1210466 }}</ref>

No data detailing signigicant function in DEPD7 has been published or recorded.
{{clear}}

== References ==
{{reflist|33em}}