Reviewed, UniProtKB/Swiss-Prot P22808 (VND_DROME)

Names and origin

Protein names

Recommended name:
    Homeobox protein vnd
Alternative name(s):
    Protein ventral nervous system defective
    Homeobox protein NK-2

Gene names

Name:	vnd
Synonyms:	NK2
ORF Names:	CG6172

Organism

Drosophila melanogaster (Fruit fly) [Complete proteome]

Taxonomic identifier

7227 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Arthropoda › Hexapoda › Insecta › Pterygota › Neoptera › Endopterygota › Diptera › Brachycera › Muscomorpha › Ephydroidea › Drosophilidae › Drosophila › Sophophora

Protein attributes

Sequence length	723 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Probable transcriptional regulator involved in the regulation of the proneural AS-C genes and the neurogenic genes of the enhancer of split complex. Could specifically activate proneural genes in the ventral-most neuroectoderm. Ref.1
Subcellular location	Nucleus Probable.
Tissue specificity	Expressed in the CNS and midgut. Ref.1
Sequence similarities	Belongs to the NK-2 homeobox family. Contains 1 homeobox DNA-binding domain.

Ontologies

Keywords
Biological process	Differentiation Neurogenesis Transcription Transcription regulation
Cellular component	Nucleus
Domain	Homeobox
Ligand	DNA-binding
Molecular function	Developmental protein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	brain development Inferred from mutant phenotype. Source: FlyBase dorsal/ventral pattern formation Traceable author statement. Source: FlyBase ectoderm development Traceable author statement. Source: FlyBase glial cell development Inferred from mutant phenotype. Source: FlyBase neuroblast development Inferred from mutant phenotype. Source: FlyBase neuroblast fate determination Inferred from mutant phenotype. Source: FlyBase positive regulation of specific transcription from RNA polymerase II promoter Inferred from direct assay. Source: FlyBase transcription Inferred from electronic annotation. Source: UniProtKB-KW ventral cord development Traceable author statement. Source: FlyBase
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	sequence-specific DNA binding Inferred from electronic annotation. Source: InterPro transcription factor activity Inferred from electronic annotation. Source: InterPro transcription factor binding Inferred from physical interaction. Source: FlyBase
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
	Q9VU16	1	EBI-171341,EBI-99531
CG10265	Q9V786	1	EBI-171341,EBI-167512

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 723

723

Homeobox protein vnd

PRO_0000049071

Regions

DNA binding

545 – 604

60

Homeobox

Compositional bias

225 – 350

126

His-rich

Compositional bias

319 – 360

42

Ala-rich

Compositional bias

483 – 493

11

Asn-rich

Compositional bias

664 – 720

57

Ala-rich

Compositional bias

675 – 715

41

His-rich

Experimental info

Mutagenesis

579

1

A → T in vnd-29; disrupts neuroblast development. Ref.1

Sequence conflict

52

1

R → A in AAB34960. Ref.2

Sequence conflict

55

1

R → P in AAB34960. Ref.2

Sequence conflict

88

1

D → E in CAA60619. Ref.1

Sequence conflict

149

1

A → R in CAA60619. Ref.1

Sequence conflict

153

1

Missing in CAA60619. Ref.1

Sequence conflict

254

1

L → V in AAB34960. Ref.2

Sequence conflict

362

1

Q → K in CAA60619. Ref.1

Sequence conflict

399

1

I → M in CAA60619. Ref.1

Sequence conflict

405

1

Y → H in CAA21410. Ref.5

Sequence conflict

610

1

E → D in CAA21410. Ref.5

Sequence conflict

633 – 634

2

RR → VG Ref.6

Secondary structure

1

.

.

.

.

.

.

.

723

Helix Strand Turn

Details...

Helix

554 – 566

13

Helix

572 – 581

10

Helix

586 – 606

21

Sequences

	Sequence		Length	Mass (Da)
	P22808-1 [UniParc]. Last modified May 10, 2004. Version 3. Checksum: 811F20B03A93C95E	FASTA	723	76,422
	10 20 30 40 50 60 MTTSASLERT PSKRDRDRER DNSSGLGSAG SLPASPQSAI TVSPSSPATP KRPLRTSTPS 70 80 90 100 110 120 LERKREREDR EDREDRKERQ ERHERDRDHE RFAAVFSTAS TTVPTNTSSS SGLAPEQLRI 130 140 150 160 170 180 PTGAAAFSGF PGLHSMSSLM LPSSAAVAAA AAAPFLPWSP ILLPPWNHAL LPAAFYPAAL 190 200 210 220 230 240 RNALPGLFDA KVPSSQRSGF HISDILNLEG SELKNAAAAA AAAAHHGSDL SHHSASESTS 250 260 270 280 290 300 GHRGQGSHTS PSALSPTPAG VSADEHHNGS GTGGGAGEAD HHSTTEHHAP PSHPQQQHPH 310 320 330 340 350 360 HQQHHHPHLL LPQQHHQQAV APLPLAHHQS GEAQSHAHAN AAAAHLLASH NAAAAAAVAA 370 380 390 400 410 420 GQYLPNLPKN FPGSFGDEMS SYHHMAQTML QHSGRSAWIK ENELYGTQQP ASPDSTSPVT 430 440 450 460 470 480 SEVSYTYIGS NCQTSPALSG DYKSYSRSAD SDALSVGDAL HTLHGSSGNG SAGGAPTAHA 490 500 510 520 530 540 LHNNNNNTTN NNNHSLKAEG INGAGSGHDD SLNEDGIEED IDDVDDADGS GGGDANGSDG 550 560 570 580 590 600 LPNKKRKRRV LFTKAQTYEL ERRFRQQRYL SAPEREHLAS LIRLTPTQVK IWFQNHRYKT 610 620 630 640 650 660 KRAQNEKGYE GHPGLLHGHA THPHHPSALP SPRRVAVPVL VRNGKPCLGD SSKLGADCVS 670 680 690 700 710 720 VSSATATAMQ NAAAHHLVAL NGAAAYQHAA AAAAGLHAHA HAHAHAHGHG HPHAHAQRAA WWP

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"vnd, a gene required for early neurogenesis of Drosophila, encodes a homeodomain protein." Jimenez F., Martin-Morris L.E., Velasco L., Chu H., Sierra J., Rosen D.R., White K. EMBO J. 14:3487-3495(1995) [PubMed: 7628450] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, MUTAGENESIS OF ALA-579.
[2]	"The NK-2 homeobox gene and the early development of the central nervous system of Drosophila." Nirenberg M., Nakayama K., Nakayama N., Kim Y., Mellerick D., Wang L.H., Webber K.O., Lad R. Ann. N. Y. Acad. Sci. 758:224-242(1995) [PubMed: 7625694] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]	"The genome sequence of Drosophila melanogaster." 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. Science 287:2185-2195(2000) [PubMed: 10731132] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Berkeley.
[4]	"Annotation of the Drosophila melanogaster euchromatic genome: a systematic review." 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. Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002) [PubMed: 12537572] [Abstract] Cited for: GENOME REANNOTATION.
[5]	"From sequence to chromosome: the tip of the X chromosome of D. melanogaster." Benos P.V., Gatt M.K., Ashburner M., Murphy L., Harris D., Barrell B.G., Ferraz C., Vidal S., Brun C., Demailles J., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Borkova D., Minana B. , Kafatos F.C., Louis C., Siden-Kiamos I., Bolshakov S., Papagiannakis G., Spanos L., Cox S., Madueno E., de Pablos B., Modolell J., Peter A., Schoettler P., Werner M., Mourkioti F., Beinert N., Dowe G., Schaefer U., Jaeckle H., Bucheton A., Callister D.M., Campbell L.A., Darlamitsou A., Henderson N.S., McMillan P.J., Salles C., Tait E.A., Valenti P., Saunders R.D.C., Glover D.M. Science 287:2220-2222(2000) [PubMed: 10731137] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Oregon-R.
[6]	"Drosophila NK-homeobox genes." Kim Y., Nirenberg M. Proc. Natl. Acad. Sci. U.S.A. 86:7716-7720(1989) [PubMed: 2573058] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 477-634. Strain: Canton-S.
[7]	"The three-dimensional solution structure of the NK-2 homeodomain from Drosophila." Tsao D.H.H., Gruschus J.M., Wang L.-H., Nirenberg M., Ferretti J.A. J. Mol. Biol. 251:297-307(1995) [PubMed: 7643404] [Abstract] Cited for: STRUCTURE BY NMR OF 538-613.
[8]	"Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity." Gruschus J.M., Tsao D.H.H., Wang L.-H., Nirenberg M., Ferretti J.A. Biochemistry 36:5372-5380(1997) [PubMed: 9154919] [Abstract] Cited for: STRUCTURE BY NMR OF 544-606.
[9]	Bosong X. Submitted (JUL-1999) to the PDB data bank Cited for: STRUCTURE BY NMR OF 533-612.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X87141 mRNA. Translation: CAA60619.1.
S78691 mRNA. Translation: AAB34960.1.
AE014298 Genomic DNA. Translation: AAF45521.1.
AL031883 Genomic DNA. Translation: CAA21410.1.
M27290 Genomic DNA. Translation: AAA28617.1.

PIR

S57246.

RefSeq

NP_476786.2.

UniGene

Dm.4713

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NK2	NMR	-	P	538-613	[»]
1NK3	NMR	-	P	538-613	[»]
1QRY	NMR	-	A	538-613	[»]
1VND	NMR	-	A	538-613	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P22808. 14 interactions.

Genome annotation databases

Ensembl

FBgn0003986. Drosophila melanogaster. [Contig view]

GeneID

31003.

NMPDR

fig|7227.3.peg.15917.

Organism-specific databases

FlyBase

FBgn0003986. vnd.

Phylogenomic databases

HOGENOM

P22808.

OMA

P22808. WIKENEL.

Enzyme and pathway databases

BioCyc

DMEL-XXX-02:DMEL-XXX-02-000044-MON.

Gene expression databases

ArrayExpress

P22808.

GermOnline

CG6172. Drosophila melanogaster.

Family and domain databases

InterPro

IPR001356. Homeobox.
IPR017970. Homeobox_CS.
IPR012287. Homeodomain-rel.
[Graphical view]

Gene3D

G3DSA:1.10.10.60. Homeodomain-rel. 1 hit.

Pfam

PF00046. Homeobox. 1 hit.
[Graphical view]

ProDom

PD000010. Homeobox. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00389. HOX. 1 hit.
[Graphical view]

PROSITE

PS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

771420.

Entry information

Entry name

VND_DROME

Accession

Primary (citable) accession number: P22808
Secondary accession number(s): Q24589 , Q26436, Q9UB43, Q9W5F0

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1991
Last sequence update:	May 10, 2004
Last modified:	June 16, 2009
This is version 93 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Drosophila annotation project