VND_DROME
ID VND_DROME Reviewed; 723 AA.
AC P22808; Q24589; Q26436; Q9UB43; Q9W5F0;
DT 01-AUG-1991, integrated into UniProtKB/Swiss-Prot.
DT 10-MAY-2004, sequence version 3.
DT 03-AUG-2022, entry version 197.
DE RecName: Full=Homeobox protein vnd;
DE AltName: Full=Homeobox protein NK-2;
DE AltName: Full=Protein ventral nervous system defective;
GN Name=vnd; Synonyms=NK2; ORFNames=CG6172;
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, AND MUTAGENESIS
RP OF ALA-579.
RX PubMed=7628450; DOI=10.1002/j.1460-2075.1995.tb07355.x;
RA Jimenez F., Martin-Morris L.E., Velasco L., Chu H., Sierra J., Rosen D.R.,
RA White K.;
RT "vnd, a gene required for early neurogenesis of Drosophila, encodes a
RT homeodomain protein.";
RL EMBO J. 14:3487-3495(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=7625694; DOI=10.1111/j.1749-6632.1995.tb24830.x;
RA Nirenberg M., Nakayama K., Nakayama N., Kim Y., Mellerick D., Wang L.H.,
RA Webber K.O., Lad R.;
RT "The NK-2 homeobox gene and the early development of the central nervous
RT system of Drosophila.";
RL Ann. N. Y. Acad. Sci. 758:224-242(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=Berkeley;
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Oregon-R;
RX PubMed=10731137; DOI=10.1126/science.287.5461.2220;
RA Benos P.V., Gatt M.K., Ashburner M., Murphy L., Harris D., Barrell B.G.,
RA Ferraz C., Vidal S., Brun C., Demailles J., Cadieu E., Dreano S., Gloux S.,
RA Lelaure V., Mottier S., Galibert F., Borkova D., Minana B., Kafatos F.C.,
RA Louis C., Siden-Kiamos I., Bolshakov S., Papagiannakis G., Spanos L.,
RA Cox S., Madueno E., de Pablos B., Modolell J., Peter A., Schoettler P.,
RA Werner M., Mourkioti F., Beinert N., Dowe G., Schaefer U., Jaeckle H.,
RA Bucheton A., Callister D.M., Campbell L.A., Darlamitsou A., Henderson N.S.,
RA McMillan P.J., Salles C., Tait E.A., Valenti P., Saunders R.D.C.,
RA Glover D.M.;
RT "From sequence to chromosome: the tip of the X chromosome of D.
RT melanogaster.";
RL Science 287:2220-2222(2000).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 477-634.
RC STRAIN=Canton-S;
RX PubMed=2573058; DOI=10.1073/pnas.86.20.7716;
RA Kim Y., Nirenberg M.;
RT "Drosophila NK-homeobox genes.";
RL Proc. Natl. Acad. Sci. U.S.A. 86:7716-7720(1989).
RN [7]
RP STRUCTURE BY NMR OF 538-613.
RX PubMed=7643404; DOI=10.1006/jmbi.1995.0435;
RA Tsao D.H.H., Gruschus J.M., Wang L.-H., Nirenberg M., Ferretti J.A.;
RT "The three-dimensional solution structure of the NK-2 homeodomain from
RT Drosophila.";
RL J. Mol. Biol. 251:297-307(1995).
RN [8]
RP STRUCTURE BY NMR OF 544-606.
RX PubMed=9154919; DOI=10.1021/bi9620060;
RA Gruschus J.M., Tsao D.H.H., Wang L.-H., Nirenberg M., Ferretti J.A.;
RT "Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic
RT resonance spectroscopy: basis of binding specificity.";
RL Biochemistry 36:5372-5380(1997).
RN [9]
RP STRUCTURE BY NMR OF 533-612.
RA Bosong X.;
RL Submitted (JUL-1999) to the PDB data bank.
CC -!- FUNCTION: Probable transcriptional regulator involved in the regulation
CC of the proneural AS-C genes and the neurogenic genes of the enhancer of
CC split complex. Could specifically activate proneural genes in the
CC ventral-most neuroectoderm. {ECO:0000269|PubMed:7628450}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Expressed in the CNS and midgut.
CC {ECO:0000269|PubMed:7628450}.
CC -!- SIMILARITY: Belongs to the NK-2 homeobox family. {ECO:0000305}.
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DR EMBL; X87141; CAA60619.1; -; mRNA.
DR EMBL; S78691; AAB34960.1; -; mRNA.
DR EMBL; AE014298; AAF45521.1; -; Genomic_DNA.
DR EMBL; AL031883; CAA21410.1; -; Genomic_DNA.
DR EMBL; M27290; AAA28617.1; -; Genomic_DNA.
DR PIR; S57246; S57246.
DR RefSeq; NP_476786.2; NM_057438.4.
DR PDB; 1NK2; NMR; -; P=538-613.
DR PDB; 1NK3; NMR; -; P=538-613.
DR PDB; 1QRY; NMR; -; A=538-613.
DR PDB; 1VND; NMR; -; A=538-613.
DR PDBsum; 1NK2; -.
DR PDBsum; 1NK3; -.
DR PDBsum; 1QRY; -.
DR PDBsum; 1VND; -.
DR AlphaFoldDB; P22808; -.
DR BMRB; P22808; -.
DR SMR; P22808; -.
DR BioGRID; 57572; 30.
DR DIP; DIP-60882N; -.
DR IntAct; P22808; 14.
DR STRING; 7227.FBpp0070105; -.
DR PaxDb; P22808; -.
DR PRIDE; P22808; -.
DR EnsemblMetazoa; FBtr0070110; FBpp0070105; FBgn0261930.
DR GeneID; 31003; -.
DR KEGG; dme:Dmel_CG6172; -.
DR CTD; 31003; -.
DR FlyBase; FBgn0261930; vnd.
DR VEuPathDB; VectorBase:FBgn0261930; -.
DR eggNOG; KOG0842; Eukaryota.
DR GeneTree; ENSGT00940000166323; -.
DR HOGENOM; CLU_023266_0_0_1; -.
DR InParanoid; P22808; -.
DR PhylomeDB; P22808; -.
DR BioGRID-ORCS; 31003; 0 hits in 3 CRISPR screens.
DR EvolutionaryTrace; P22808; -.
DR GenomeRNAi; 31003; -.
DR PRO; PR:P22808; -.
DR Proteomes; UP000000803; Chromosome X.
DR Bgee; FBgn0261930; Expressed in ventral nerve cord primordium (Drosophila) and 44 other tissues.
DR ExpressionAtlas; P22808; baseline and differential.
DR Genevisible; P22808; DM.
DR GO; GO:0005634; C:nucleus; IDA:FlyBase.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IDA:FlyBase.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0008134; F:transcription factor binding; IPI:FlyBase.
DR GO; GO:0007420; P:brain development; IMP:FlyBase.
DR GO; GO:0030154; P:cell differentiation; IBA:GO_Central.
DR GO; GO:0021782; P:glial cell development; IMP:FlyBase.
DR GO; GO:0010629; P:negative regulation of gene expression; IMP:FlyBase.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:FlyBase.
DR GO; GO:0014019; P:neuroblast development; IMP:FlyBase.
DR GO; GO:0007400; P:neuroblast fate determination; IMP:FlyBase.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IDA:FlyBase.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IMP:FlyBase.
DR CDD; cd00086; homeodomain; 1.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR017970; Homeobox_CS.
DR InterPro; IPR001356; Homeobox_dom.
DR Pfam; PF00046; Homeodomain; 1.
DR SMART; SM00389; HOX; 1.
DR SUPFAM; SSF46689; SSF46689; 1.
DR PROSITE; PS00027; HOMEOBOX_1; 1.
DR PROSITE; PS50071; HOMEOBOX_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Developmental protein; Differentiation; DNA-binding;
KW Homeobox; Neurogenesis; Nucleus; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..723
FT /note="Homeobox protein vnd"
FT /id="PRO_0000049071"
FT DNA_BIND 545..604
FT /note="Homeobox"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00108"
FT REGION 1..115
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 224..307
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 465..549
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 703..723
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 9..23
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 24..56
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 57..93
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 95..115
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 233..257
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 465..499
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 513..529
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 579
FT /note="A->T: In vnd-29; disrupts neuroblast development."
FT /evidence="ECO:0000269|PubMed:7628450"
FT CONFLICT 52
FT /note="R -> A (in Ref. 2; AAB34960)"
FT /evidence="ECO:0000305"
FT CONFLICT 55
FT /note="R -> P (in Ref. 2; AAB34960)"
FT /evidence="ECO:0000305"
FT CONFLICT 88
FT /note="D -> E (in Ref. 1; CAA60619)"
FT /evidence="ECO:0000305"
FT CONFLICT 149
FT /note="A -> R (in Ref. 1; CAA60619)"
FT /evidence="ECO:0000305"
FT CONFLICT 153
FT /note="Missing (in Ref. 1; CAA60619)"
FT /evidence="ECO:0000305"
FT CONFLICT 254
FT /note="L -> V (in Ref. 2; AAB34960)"
FT /evidence="ECO:0000305"
FT CONFLICT 362
FT /note="Q -> K (in Ref. 1; CAA60619)"
FT /evidence="ECO:0000305"
FT CONFLICT 399
FT /note="I -> M (in Ref. 1; CAA60619)"
FT /evidence="ECO:0000305"
FT CONFLICT 405
FT /note="Y -> H (in Ref. 5; CAA21410)"
FT /evidence="ECO:0000305"
FT CONFLICT 610
FT /note="E -> D (in Ref. 5; CAA21410)"
FT /evidence="ECO:0000305"
FT CONFLICT 633..634
FT /note="RR -> VG (in Ref. 6)"
FT /evidence="ECO:0000305"
FT STRAND 542..545
FT /evidence="ECO:0007829|PDB:1VND"
FT HELIX 554..566
FT /evidence="ECO:0007829|PDB:1NK2"
FT HELIX 572..581
FT /evidence="ECO:0007829|PDB:1NK2"
FT HELIX 586..606
FT /evidence="ECO:0007829|PDB:1NK2"
FT STRAND 608..611
FT /evidence="ECO:0007829|PDB:1QRY"
SQ SEQUENCE 723 AA; 76422 MW; 811F20B03A93C95E CRC64;
MTTSASLERT PSKRDRDRER DNSSGLGSAG SLPASPQSAI TVSPSSPATP KRPLRTSTPS
LERKREREDR EDREDRKERQ ERHERDRDHE RFAAVFSTAS TTVPTNTSSS SGLAPEQLRI
PTGAAAFSGF PGLHSMSSLM LPSSAAVAAA AAAPFLPWSP ILLPPWNHAL LPAAFYPAAL
RNALPGLFDA KVPSSQRSGF HISDILNLEG SELKNAAAAA AAAAHHGSDL SHHSASESTS
GHRGQGSHTS PSALSPTPAG VSADEHHNGS GTGGGAGEAD HHSTTEHHAP PSHPQQQHPH
HQQHHHPHLL LPQQHHQQAV APLPLAHHQS GEAQSHAHAN AAAAHLLASH NAAAAAAVAA
GQYLPNLPKN FPGSFGDEMS SYHHMAQTML QHSGRSAWIK ENELYGTQQP ASPDSTSPVT
SEVSYTYIGS NCQTSPALSG DYKSYSRSAD SDALSVGDAL HTLHGSSGNG SAGGAPTAHA
LHNNNNNTTN NNNHSLKAEG INGAGSGHDD SLNEDGIEED IDDVDDADGS GGGDANGSDG
LPNKKRKRRV LFTKAQTYEL ERRFRQQRYL SAPEREHLAS LIRLTPTQVK IWFQNHRYKT
KRAQNEKGYE GHPGLLHGHA THPHHPSALP SPRRVAVPVL VRNGKPCLGD SSKLGADCVS
VSSATATAMQ NAAAHHLVAL NGAAAYQHAA AAAAGLHAHA HAHAHAHGHG HPHAHAQRAA
WWP
