P06601 (PRD_DROME) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Segmentation protein paired

Gene names

Name:	prd
ORF Names:	CG6716

Organism

Drosophila melanogaster (Fruit fly) [Reference proteome]

Taxonomic identifier

7227 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Protostomia › Ecdysozoa › Panarthropoda › Arthropoda › Mandibulata › Pancrustacea › Hexapoda › Insecta › Dicondylia › Pterygota › Neoptera › Endopterygota › Diptera › Brachycera › Muscomorpha › Eremoneura › Cyclorrhapha › Schizophora › Acalyptratae › Ephydroidea › Drosophilidae › Drosophilinae › Drosophilini › Drosophilina › Drosophiliti › Drosophila › Sophophora › melanogaster group › melanogaster subgroup

Protein attributes

Sequence length	613 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Pair-rule protein expressed in a segmentally repeating pattern to define the polarity of embryonic segments. Capable of sequence-specific DNA-binding.
Subcellular location	Nucleus.
Sequence similarities	Belongs to the paired homeobox family. Contains 1 homeobox DNA-binding domain. Contains 1 paired domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Homeobox Paired box Repeat
Ligand	DNA-binding
Molecular function	Developmental protein Pair-rule protein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	periodic partitioning by pair rule gene Non-traceable author statement Ref.1. Source: UniProtKB positive regulation of transcription from RNA polymerase II promoter Inferred from direct assay PubMed 10885752. Source: FlyBase
Cellular_component	nucleus Non-traceable author statement Ref.1. Source: UniProtKB
Molecular_function	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity Inferred from direct assay PubMed 10885752. Source: FlyBase RNA polymerase II regulatory region sequence-specific DNA binding Inferred from direct assay PubMed 7906390. Source: FlyBase
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform B (identifier: P06601-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform A (identifier: P06601-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-23: Missing.

Note: No experimental confirmation available.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 613

613

Segmentation protein paired

PRO_0000050167

Regions

Domain

27 – 153

127

Paired

DNA binding

213 – 272

60

Homeobox

Compositional bias

541 – 576

36

His/Pro-rich

Natural variations

Alternative sequence

1 – 23

23

Missing in isoform A.

VSP_007021

Natural variant

164

1

A → T.

Natural variant

220

1

F → I.

Secondary structure

1

.

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613

Helix Strand Turn

Details...

Beta strand

29 – 31

3

Beta strand

37 – 39

3

Helix

46 – 57

12

Helix

62 – 69

8

Helix

73 – 86

14

Helix

106 – 112

7

Turn

113 – 116

4

Helix

122 – 131

10

Beta strand

133 – 135

3

Helix

143 – 149

7

Helix

222 – 234

13

Helix

240 – 250

11

Helix

254 – 275

22

Sequences

	Sequence		Length	Mass (Da)
	Isoform B [UniParc]. Last modified January 1, 1988. Version 1. Checksum: 777772C6E704C1A2	FASTA	613	65,497
	10 20 30 40 50 60 MTVTAFAAAM HRPFFNGYST MQDMNSGQGR VNQLGGVFIN GRPLPNNIRL KIVEMAADGI 70 80 90 100 110 120 RPCVISRQLR VSHGCVSKIL NRYQETGSIR PGVIGGSKPR IATPEIENRI EEYKRSSPGM 130 140 150 160 170 180 FSWEIREKLI REGVCDRSTA PSVSAISRLV RGRDAPLDND MSSASGSPAG DGTKASSSCG 190 200 210 220 230 240 SDVSGGHHNN GKPSDEDISD CESEPGIALK RKQRRCRTTF SASQLDELER AFERTQYPDI 250 260 270 280 290 300 YTREELAQRT NLTEARIQVW FSNRRARLRK QHTSVSGGAP GGAAASVSHV AASSSLPSVV 310 320 330 340 350 360 SSVPSMAPLA MMPGSLDPAT VYQQQYDFYG SHANISVSAA APMASSNLSP GITTTPPHHH 370 380 390 400 410 420 QFYNPSANTA SYIMPGENGN TTPTGNIIVS SYETQLGSVY GTETETHQTM PRNESPNESV 430 440 450 460 470 480 SSAFGQLPPT PNSLSAVVSG AGVTSSSGAN SGADPSQSLA NASAGSEELS AALKVESVDL 490 500 510 520 530 540 IAASQSQLYG GWSSMQALRP NAPLSPEDSL NSTSSTSQAL DVTAHQMFHP YQHTPQYASY 550 560 570 580 590 600 PAPGHAHSHH GHPHAPHPHA HPHPQYAGAH PHYPPPSSSA HFMPQNFNAA AFPSPSKVNY 610 TTMPPQPFYP SWY
	Isoform A [UniParc]. Checksum: D4B391B51DE7FF06	FASTA	590	62,920
	10 20 30 40 50 60 MNSGQGRVNQ LGGVFINGRP LPNNIRLKIV EMAADGIRPC VISRQLRVSH GCVSKILNRY 70 80 90 100 110 120 QETGSIRPGV IGGSKPRIAT PEIENRIEEY KRSSPGMFSW EIREKLIREG VCDRSTAPSV 130 140 150 160 170 180 SAISRLVRGR DAPLDNDMSS ASGSPAGDGT KASSSCGSDV SGGHHNNGKP SDEDISDCES 190 200 210 220 230 240 EPGIALKRKQ RRCRTTFSAS QLDELERAFE RTQYPDIYTR EELAQRTNLT EARIQVWFSN 250 260 270 280 290 300 RRARLRKQHT SVSGGAPGGA AASVSHVAAS SSLPSVVSSV PSMAPLAMMP GSLDPATVYQ 310 320 330 340 350 360 QQYDFYGSHA NISVSAAAPM ASSNLSPGIT TTPPHHHQFY NPSANTASYI MPGENGNTTP 370 380 390 400 410 420 TGNIIVSSYE TQLGSVYGTE TETHQTMPRN ESPNESVSSA FGQLPPTPNS LSAVVSGAGV 430 440 450 460 470 480 TSSSGANSGA DPSQSLANAS AGSEELSAAL KVESVDLIAA SQSQLYGGWS SMQALRPNAP 490 500 510 520 530 540 LSPEDSLNST SSTSQALDVT AHQMFHPYQH TPQYASYPAP GHAHSHHGHP HAPHPHAHPH 550 560 570 580 590 PQYAGAHPHY PPPSSSAHFM PQNFNAAAFP SPSKVNYTTM PPQPFYPSWY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structure of the segmentation gene paired and the Drosophila PRD gene set as part of a gene network." Frigerio G., Burri M., Bopp D., Baumgartner S., Noll M. Cell 47:735-746(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM B).
[2]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Berkeley.
[3]	"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] [Europe PMC] [Abstract] Cited for: GENOME REANNOTATION, ALTERNATIVE SPLICING. Strain: Berkeley.
[4]	"A Drosophila full-length cDNA resource." 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. Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM A). Strain: Berkeley. Tissue: Head.
[5]	"Crystal structure of a paired domain-DNA complex at 2.5-A resolution reveals structural basis for Pax developmental mutations." Xu W., Rould M.A., Jun S., Desplan C., Pabo C.O. Cell 80:639-650(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 27-154.
[6]	"High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA." Wilson D.S., Guenther B., Desplan C., Kuriyan J. Cell 82:709-719(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 196-276.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M14548 Genomic DNA. Translation: AAB59221.1.
AE014134 Genomic DNA. Translation: AAN10801.1.
AE014134 Genomic DNA. Translation: AAF53160.1.
AY059447 mRNA. Translation: AAL13353.1.

PIR

A26062.

RefSeq

NP_523556.1. NM_078832.2.
NP_723721.1. NM_164990.2.

UniGene

Dm.2598.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FJL	X-ray	2.00	A/B/C	196-276	[»]
1PDN	X-ray	2.50	C	27-154	[»]

ProteinModelPortal

P06601.

SMR

P06601. Positions 28-150, 212-276.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-22888N.

STRING

7227.FBpp0079882.

Proteomic databases

PRIDE

P06601.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblMetazoa

FBtr0080298; FBpp0079882; FBgn0003145.

GeneID

34629.

KEGG

dme:Dmel_CG6716.

UCSC

CG6716-RA. d. melanogaster.

Organism-specific databases

CTD

5548.

FlyBase

FBgn0003145. prd.

Phylogenomic databases

eggNOG

NOG326044.

GeneTree

ENSGT00680000099553.

InParanoid

P06601.

KO

K09381.

OMA

TASYIMP.

OrthoDB

EOG42BVRM.

PhylomeDB

P06601.

Enzyme and pathway databases

SignaLink

P06601.

Gene expression databases

Bgee

P06601.

GermOnline

CG6716. Drosophila melanogaster.

Family and domain databases

Gene3D

1.10.10.10. 2 hits.
1.10.10.60. 1 hit.

InterPro

IPR017970. Homeobox_CS.
IPR001356. Homeodomain.
IPR009057. Homeodomain-like.
IPR001523. Paired_dom.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]

Pfam

PF00046. Homeobox. 1 hit.
PF00292. PAX. 1 hit.
[Graphical view]

PRINTS

PR00027. PAIREDBOX.

SMART

SM00389. HOX. 1 hit.
SM00351. PAX. 1 hit.
[Graphical view]

SUPFAM

SSF46689. Homeodomain_like. 2 hits.

PROSITE

PS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00034. PAIRED_1. 1 hit.
PS51057. PAIRED_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P06601.

GenomeRNAi

34629.

NextBio

789399.

Entry information

Entry name

PRD_DROME

Accession

Primary (citable) accession number: P06601
Secondary accession number(s): Q9VKB6

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1988
Last sequence update:	January 1, 1988
Last modified:	May 29, 2013
This is version 137 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Drosophila annotation project