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Homeotic protein bicoid (PRD-4)

 BCD_DROME               Reviewed;         494 AA.
P09081; Q5BI92; Q86BA9; Q86BP2; Q8INR7; Q8ST46; Q8STB1; Q8T9S9;
Q8T9T0; Q8T9T1; Q95TN3; Q9UAM0; Q9VI47;
01-NOV-1988, integrated into UniProtKB/Swiss-Prot.
10-MAY-2004, sequence version 3.
27-SEP-2017, entry version 183.
RecName: Full=Homeotic protein bicoid;
AltName: Full=PRD-4;
Name=bcd; ORFNames=CG1034;
Drosophila melanogaster (Fruit fly).
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta;
Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha;
Ephydroidea; Drosophilidae; Drosophila; Sophophora.
NCBI_TaxID=7227;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORMS A; D AND G).
STRAIN=Oregon-R; TISSUE=Embryo;
PubMed=2901954;
Berleth T., Burri M., Thoma G., Bopp D., Richstein S., Frigerio G.,
Noll M., Nuesslein-Volhard C.;
"The role of localization of bicoid RNA in organizing the anterior
pattern of the Drosophila embryo.";
EMBO J. 7:1749-1756(1988).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM D), AND VARIANTS.
STRAIN=Z116, Z131, Z145, Z157, Z159, Z184, Z186, Z191, Z194, Z196,
Z197, Z209, Z210, Z212, Z216, Z229, Z266, Z346, Z362, Z377, Z384,
Z398, Z82, Z84, and Z95;
PubMed=12082119; DOI=10.1093/oxfordjournals.molbev.a004179;
Baines J.F., Chen Y., Das A., Stephan W.;
"DNA sequence variation at a duplicated gene: excess of replacement
polymorphism and extensive haplotype structure in the Drosophila
melanogaster bicoid region.";
Mol. Biol. Evol. 19:989-998(2002).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Berkeley;
Celniker S.E., Pfeiffer B., Knafels J., Martin C.H., Mayeda C.A.,
Palazzolo M.J.;
"Complete sequence of the Antennapedia complex of Drosophila.";
Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Berkeley;
PubMed=10731132; DOI=10.1126/science.287.5461.2185;
Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X.,
Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D.,
Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G.,
Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D.,
Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M.,
Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S.,
Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P.,
Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I.,
Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P.,
de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M.,
Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P.,
Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W.,
Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K.,
Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J.,
Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C.,
Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A.,
Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z.,
Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X.,
Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D.,
Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A.,
Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L.,
Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M.,
Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G.,
Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H.,
Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
Spier E., Spradling A.C., Stapleton M., Strong R., Sun E.,
Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X.,
Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J.,
Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A.,
Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L.,
Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X.,
Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C.;
"The genome sequence of Drosophila melanogaster.";
Science 287:2185-2195(2000).
[5]
GENOME REANNOTATION, AND ALTERNATIVE SPLICING.
STRAIN=Berkeley;
PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q.,
Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M.,
Lewis S.E.;
"Annotation of the Drosophila melanogaster euchromatic genome: a
systematic review.";
Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM D).
STRAIN=Berkeley; TISSUE=Embryo;
PubMed=12537569; DOI=10.1186/gb-2002-3-12-research0080;
Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M.,
George R.A., Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H.,
Rubin G.M., Celniker S.E.;
"A Drosophila full-length cDNA resource.";
Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002).
[7]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM G).
STRAIN=Berkeley; TISSUE=Embryo;
Stapleton M., Carlson J.W., Chavez C., Frise E., George R.A.,
Pacleb J.M., Park S., Wan K.H., Yu C., Rubin G.M., Celniker S.E.;
Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
[8]
NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] OF 12-47 AND 86-156 (ISOFORMS
D/G).
PubMed=2877746; DOI=10.1016/0092-8674(86)90516-7;
Frigerio G., Burri M., Bopp D., Baumgartner S., Noll M.;
"Structure of the segmentation gene paired and the Drosophila PRD gene
set as part of a gene network.";
Cell 47:735-746(1986).
[9]
POSSIBLE RNA-BINDING DOMAIN.
PubMed=2752425; DOI=10.1016/0092-8674(89)90834-9;
Rebagliati M.;
"An RNA recognition motif in the bicoid protein.";
Cell 58:231-232(1989).
[10]
INTERACTION WITH BIN3.
PubMed=10717484; DOI=10.1016/S0378-1119(00)00048-2;
Zhu W., Hanes S.D.;
"Identification of Drosophila bicoid-interacting proteins using a
custom two-hybrid selection.";
Gene 245:329-339(2000).
[11]
INTERACTION WITH BIN1.
PubMed=11455422; DOI=10.1007/s004270100135;
Zhu W., Foehr M., Jaynes J.B., Hanes S.D.;
"Drosophila SAP18, a member of the Sin3/Rpd3 histone deacetylase
complex, interacts with Bicoid and inhibits its activity.";
Dev. Genes Evol. 211:109-117(2001).
-!- FUNCTION: Segment polarity protein that provides positional cues
for the development of head and thoracic segments. Regulates the
expression of zygotic genes, possibly through its homeodomain, and
inhibits the activity of other maternal gene products. May also
bind RNA. Interacts with Bin1 to repress transcription of bicoid
target genes in the anterior tip of the embryo; a process known as
retraction.
-!- SUBUNIT: Interacts with Bin1; in vitro and yeast cells. Interacts
with bin3. {ECO:0000269|PubMed:10717484,
ECO:0000269|PubMed:11455422}.
-!- INTERACTION:
Q9VEX9:Bin1; NbExp=2; IntAct=EBI-196628, EBI-129424;
Q7K480:bin3; NbExp=4; IntAct=EBI-196628, EBI-180984;
O97102:smt3; NbExp=3; IntAct=EBI-196628, EBI-114439;
-!- SUBCELLULAR LOCATION: Nucleus.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=5;
Name=G;
IsoId=P09081-1; Sequence=Displayed;
Name=A;
IsoId=P09081-3; Sequence=VSP_002235;
Name=D;
IsoId=P09081-2; Sequence=VSP_002234;
Name=E;
IsoId=P09081-4; Sequence=VSP_027203;
Note=No experimental confirmation available.;
Name=F;
IsoId=P09081-5; Sequence=VSP_027203, VSP_002234;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: Maternal expression is an anterior cap
concentrated in the cortical cytoplasm.
-!- DEVELOPMENTAL STAGE: Expressed both maternally and zygotically.
-!- SIMILARITY: Belongs to the paired homeobox family. Bicoid
subfamily. {ECO:0000305}.
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EMBL; X07870; CAA30720.1; -; Genomic_DNA.
EMBL; X14458; CAA32627.1; -; mRNA.
EMBL; X14459; CAB37631.1; -; mRNA.
EMBL; X14460; CAA32629.1; -; mRNA.
EMBL; AF466621; AAL77008.1; -; Genomic_DNA.
EMBL; AF466622; AAL77009.1; -; Genomic_DNA.
EMBL; AF466623; AAL77010.1; -; Genomic_DNA.
EMBL; AF466624; AAL77011.1; -; Genomic_DNA.
EMBL; AF466625; AAL77012.1; -; Genomic_DNA.
EMBL; AF466626; AAL77013.1; -; Genomic_DNA.
EMBL; AF466627; AAL77014.1; -; Genomic_DNA.
EMBL; AF466628; AAL77015.1; -; Genomic_DNA.
EMBL; AF466629; AAL77016.1; -; Genomic_DNA.
EMBL; AF466630; AAL77017.1; -; Genomic_DNA.
EMBL; AF466631; AAL77018.1; -; Genomic_DNA.
EMBL; AF466632; AAL77019.1; -; Genomic_DNA.
EMBL; AF466633; AAL77020.1; -; Genomic_DNA.
EMBL; AF466634; AAL77021.1; -; Genomic_DNA.
EMBL; AF466635; AAL77022.1; -; Genomic_DNA.
EMBL; AF466636; AAL77023.1; -; Genomic_DNA.
EMBL; AF466637; AAL77024.1; -; Genomic_DNA.
EMBL; AF466638; AAL77025.1; -; Genomic_DNA.
EMBL; AF466639; AAL77026.1; -; Genomic_DNA.
EMBL; AF466640; AAL77027.1; -; Genomic_DNA.
EMBL; AF466641; AAL77028.1; -; Genomic_DNA.
EMBL; AF466642; AAL77029.1; -; Genomic_DNA.
EMBL; AF466643; AAL77030.1; -; Genomic_DNA.
EMBL; AF466644; AAL77031.1; -; Genomic_DNA.
EMBL; AF466645; AAL77032.1; -; Genomic_DNA.
EMBL; AE001572; AAD19798.1; -; Genomic_DNA.
EMBL; AE014297; AAF54085.2; -; Genomic_DNA.
EMBL; AE014297; AAN13368.1; -; Genomic_DNA.
EMBL; AE014297; AAN13369.1; -; Genomic_DNA.
EMBL; AE014297; AAN13371.2; -; Genomic_DNA.
EMBL; AE014297; AAO41514.1; -; Genomic_DNA.
EMBL; AY058658; AAL13887.1; -; mRNA.
EMBL; BT021332; AAX33480.1; -; mRNA.
EMBL; M14549; AAA28385.1; -; Genomic_DNA.
EMBL; K03517; AAA28391.1; -; mRNA.
PIR; S00835; WJFFBC.
RefSeq; NP_476825.1; NM_057477.5. [P09081-3]
RefSeq; NP_731111.1; NM_169157.3. [P09081-2]
RefSeq; NP_731113.2; NM_169159.4. [P09081-4]
RefSeq; NP_788587.1; NM_176410.3. [P09081-1]
RefSeq; NP_788588.1; NM_176411.3. [P09081-5]
UniGene; Dm.3237; -.
PDB; 1ZQ3; NMR; -; P=97-163.
PDBsum; 1ZQ3; -.
ProteinModelPortal; P09081; -.
SMR; P09081; -.
BioGrid; 66028; 79.
IntAct; P09081; 57.
MINT; MINT-302540; -.
STRING; 7227.FBpp0081168; -.
PaxDb; P09081; -.
PRIDE; P09081; -.
EnsemblMetazoa; FBtr0081664; FBpp0081164; FBgn0000166. [P09081-3]
EnsemblMetazoa; FBtr0081665; FBpp0081165; FBgn0000166. [P09081-2]
EnsemblMetazoa; FBtr0081666; FBpp0081166; FBgn0000166. [P09081-4]
EnsemblMetazoa; FBtr0081667; FBpp0081167; FBgn0000166. [P09081-5]
EnsemblMetazoa; FBtr0081668; FBpp0081168; FBgn0000166. [P09081-1]
GeneID; 40830; -.
KEGG; dme:Dmel_CG1034; -.
CTD; 40830; -.
FlyBase; FBgn0000166; bcd.
eggNOG; ENOG410KBMY; Eukaryota.
eggNOG; ENOG4110N46; LUCA.
InParanoid; P09081; -.
KO; K18659; -.
OMA; QFAYCFN; -.
OrthoDB; EOG091G0CRZ; -.
PhylomeDB; P09081; -.
SignaLink; P09081; -.
EvolutionaryTrace; P09081; -.
GenomeRNAi; 40830; -.
PRO; PR:P09081; -.
Proteomes; UP000000803; Chromosome 3R.
Bgee; FBgn0000166; -.
Genevisible; P09081; DM.
GO; GO:0005634; C:nucleus; IC:FlyBase.
GO; GO:0016015; F:morphogen activity; NAS:FlyBase.
GO; GO:0003730; F:mRNA 3'-UTR binding; IMP:FlyBase.
GO; GO:0043565; F:sequence-specific DNA binding; IEA:InterPro.
GO; GO:0003705; F:transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding; IDA:FlyBase.
GO; GO:0003700; F:transcription factor activity, sequence-specific DNA binding; IDA:FlyBase.
GO; GO:0045182; F:translation regulator activity; TAS:FlyBase.
GO; GO:0030371; F:translation repressor activity; IGI:FlyBase.
GO; GO:0007355; P:anterior region determination; IMP:FlyBase.
GO; GO:0009948; P:anterior/posterior axis specification; TAS:FlyBase.
GO; GO:0008595; P:anterior/posterior axis specification, embryo; TAS:FlyBase.
GO; GO:0008358; P:maternal determination of anterior/posterior axis, embryo; TAS:FlyBase.
GO; GO:0017148; P:negative regulation of translation; IMP:FlyBase.
GO; GO:0048477; P:oogenesis; IMP:FlyBase.
GO; GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; IDA:FlyBase.
GO; GO:0006357; P:regulation of transcription from RNA polymerase II promoter; NAS:FlyBase.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IMP:FlyBase.
GO; GO:0006417; P:regulation of translation; TAS:FlyBase.
GO; GO:0007367; P:segment polarity determination; IMP:FlyBase.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
CDD; cd00086; homeodomain; 1.
Gene3D; 2.130.10.10; -; 1.
InterPro; IPR009057; Homeobox-like.
InterPro; IPR017970; Homeobox_CS.
InterPro; IPR001356; Homeobox_dom.
InterPro; IPR015943; WD40/YVTN_repeat-like_dom.
Pfam; PF00046; Homeobox; 1.
SMART; SM00389; HOX; 1.
SUPFAM; SSF46689; SSF46689; 1.
PROSITE; PS00027; HOMEOBOX_1; 1.
PROSITE; PS50071; HOMEOBOX_2; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Complete proteome;
Developmental protein; DNA-binding; Homeobox; Nucleus; Polymorphism;
Reference proteome; RNA-binding; Transcription;
Transcription regulation.
CHAIN 1 494 Homeotic protein bicoid.
/FTId=PRO_0000049014.
DNA_BIND 97 156 Homeobox. {ECO:0000255|PROSITE-
ProRule:PRU00108}.
REGION 433 440 RNA-binding. {ECO:0000250}.
COMPBIAS 12 40 His/Pro-rich (PRD motif).
COMPBIAS 260 294 Gln/His-rich (OPA repeat).
VAR_SEQ 1 76 Missing (in isoform E and isoform F).
{ECO:0000305}.
/FTId=VSP_027203.
VAR_SEQ 56 400 Missing (in isoform A).
{ECO:0000303|PubMed:2901954}.
/FTId=VSP_002235.
VAR_SEQ 81 85 Missing (in isoform D and isoform F).
{ECO:0000303|PubMed:12537569,
ECO:0000303|PubMed:2901954}.
/FTId=VSP_002234.
VARIANT 284 284 Q -> H (in strain: Z362).
VARIANT 317 317 E -> K (in strain: Z229).
VARIANT 337 337 A -> S (in strain: Z95, Z197 and Z229).
VARIANT 438 438 A -> P (in strain: Z184, Z210 and Z216).
VARIANT 458 458 V -> L (in strain: Z157).
VARIANT 460 460 M -> L (in strain: Oregon-R, Z145, Z266,
Z346 and Z398).
CONFLICT 298 298 F -> S (in Ref. 1; CAB37631).
{ECO:0000305}.
HELIX 106 116 {ECO:0000244|PDB:1ZQ3}.
HELIX 124 134 {ECO:0000244|PDB:1ZQ3}.
HELIX 138 157 {ECO:0000244|PDB:1ZQ3}.
SEQUENCE 494 AA; 54511 MW; 561D8509D5C11FD3 CRC64;
MAQPPPDQNF YHHPLPHTHT HPHPHSHPHP HSHPHPHHQH PQLQLPPQFR NPFDLLFDER
TGAINYNYIR PYLPNQMPKP DVFPSEELPD SLVMRRPRRT RTTFTSSQIA ELEQHFLQGR
YLTAPRLADL SAKLALGTAQ VKIWFKNRRR RHKIQSDQHK DQSYEGMPLS PGMKQSDGDP
PSLQTLSLGG GATPNALTPS PTPSTPTAHM TEHYSESFNA YYNYNGGHNH AQANRHMHMQ
YPSGGGPGPG STNVNGGQFF QQQQVHNHQQ QLHHQGNHVP HQMQQQQQQA QQQQYHHFDF
QQKQASACRV LVKDEPEADY NFNSSYYMRS GMSGATASAS AVARGAASPG SEVYEPLTPK
NDESPSLCGI GIGGPCAIAV GETEAADDMD DGTSKKTTLQ ILEPLKGLDK SCDDGSSDDM
STGIRALAGT GNRGAAFAKF GKPSPPQGPQ PPLGMGGVAM GESNQYQCTM DTIMQAYNPH
RNAAGNSQFA YCFN


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