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Protein

Dihydropyrimidinase-related protein 3

Gene

DPYSL3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance, neuronal growth cone collapse and cell migration (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Enzyme and pathway databases

ReactomeiREACT_19199. CRMPs in Sema3A signaling.

Protein family/group databases

MEROPSiM38.976.

Names & Taxonomyi

Protein namesi
Recommended name:
Dihydropyrimidinase-related protein 3
Short name:
DRP-3
Alternative name(s):
Collapsin response mediator protein 4
Short name:
CRMP-4
Unc-33-like phosphoprotein 1
Short name:
ULIP-1
Gene namesi
Name:DPYSL3
Synonyms:CRMP4, DRP3, ULIP, ULIP1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:3015. DPYSL3.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell projection, Cytoplasm

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA27473.

Polymorphism and mutation databases

BioMutaiDPYSL3.
DMDMi3122050.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 570570Dihydropyrimidinase-related protein 3PRO_0000165917Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei32 – 321PhosphotyrosineBy similarity
Modified residuei101 – 1011PhosphothreonineBy similarity
Modified residuei102 – 1021PhosphothreonineBy similarity
Modified residuei258 – 2581N6-succinyllysineBy similarity
Modified residuei259 – 2591Phosphoserine1 Publication
Modified residuei316 – 3161Nitrated tyrosineBy similarity
Modified residuei431 – 4311PhosphotyrosineBy similarity
Modified residuei499 – 4991PhosphotyrosineBy similarity
Modified residuei509 – 5091Phosphothreonine; by GSK33 Publications
Modified residuei514 – 5141Phosphothreonine; by GSK32 Publications
Modified residuei518 – 5181Phosphoserine; by GSK31 Publication
Modified residuei522 – 5221Phosphoserine; by DYRK23 Publications
Isoform LCRMP-4 (identifier: Q14195-2)
Modified residuei102 – 1021Phosphoserine3 Publications

Post-translational modificationi

Phosphorylation on Ser-522 by DYRK2 promotes subsequent phosphorylation on Thr-509, Thr-514 and Ser-518 by GSK3.1 Publication

Keywords - PTMi

Nitration, Phosphoprotein

Proteomic databases

MaxQBiQ14195.
PaxDbiQ14195.
PRIDEiQ14195.

2D gel databases

REPRODUCTION-2DPAGEQ14195.
UCD-2DPAGEQ14195.

PTM databases

PhosphoSiteiQ14195.

Expressioni

Tissue specificityi

Mainly expressed in heart and skeletal muscle. Also strongly expressed in fetal brain and spinal cord.

Gene expression databases

BgeeiQ14195.
CleanExiHS_DPYSL3.
ExpressionAtlasiQ14195. baseline and differential.
GenevisibleiQ14195. HS.

Organism-specific databases

HPAiHPA010948.

Interactioni

Subunit structurei

Homotetramer, and heterotetramer with CRMP1, DPYSL2, DPYSL4 or DPYSL5. Interacts with synaptic vesicle protein 2 and SH3A domain of intersectin.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
CRMP1Q141943EBI-10232496,EBI-473101
DPYSL2Q165553EBI-10232496,EBI-1104711

Protein-protein interaction databases

BioGridi108143. 30 interactions.
IntActiQ14195. 4 interactions.
STRINGi9606.ENSP00000343690.

Structurei

Secondary structure

1
570
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi17 – 259Combined sources
Beta strandi30 – 389Combined sources
Beta strandi41 – 488Combined sources
Beta strandi56 – 594Combined sources
Beta strandi64 – 674Combined sources
Beta strandi69 – 746Combined sources
Helixi89 – 9810Combined sources
Beta strandi101 – 1088Combined sources
Helixi116 – 13015Combined sources
Beta strandi132 – 14110Combined sources
Helixi146 – 15813Combined sources
Beta strandi163 – 1686Combined sources
Turni171 – 1744Combined sources
Helixi178 – 19114Combined sources
Beta strandi194 – 1985Combined sources
Helixi202 – 21413Combined sources
Helixi221 – 2255Combined sources
Helixi229 – 24517Combined sources
Beta strandi250 – 2556Combined sources
Helixi258 – 27013Combined sources
Beta strandi274 – 2796Combined sources
Helixi280 – 2845Combined sources
Helixi287 – 2915Combined sources
Helixi295 – 3006Combined sources
Helixi313 – 32210Combined sources
Helixi338 – 3414Combined sources
Helixi342 – 3443Combined sources
Helixi348 – 3503Combined sources
Turni358 – 3603Combined sources
Helixi361 – 3699Combined sources
Turni370 – 3734Combined sources
Helixi377 – 3848Combined sources
Helixi386 – 3916Combined sources
Turni395 – 3973Combined sources
Beta strandi409 – 41911Combined sources
Turni422 – 4243Combined sources
Beta strandi426 – 4283Combined sources
Turni433 – 4364Combined sources
Beta strandi438 – 44811Combined sources
Beta strandi451 – 4555Combined sources
Helixi476 – 48712Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4BKNX-ray2.10A/B1-570[»]
4CNSX-ray2.40A/B/C/D13-490[»]
4CNTX-ray2.65A/B/C/D1-570[»]
4CNUX-ray2.80A/B1-570[»]
ProteinModelPortaliQ14195.
SMRiQ14195. Positions 12-497.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0044.
GeneTreeiENSGT00760000119241.
HOGENOMiHOG000219145.
HOVERGENiHBG000806.
InParanoidiQ14195.
OMAiGFHLMIS.
OrthoDBiEOG7SJD48.
PhylomeDBiQ14195.
TreeFamiTF314706.

Family and domain databases

Gene3Di2.30.40.10. 2 hits.
InterProiIPR006680. Amidohydro_1.
IPR030628. DRP3.
IPR011778. Hydantoinase/dihydroPyrase.
IPR011059. Metal-dep_hydrolase_composite.
[Graphical view]
PANTHERiPTHR11647:SF57. PTHR11647:SF57. 1 hit.
PfamiPF01979. Amidohydro_1. 1 hit.
[Graphical view]
SUPFAMiSSF51338. SSF51338. 2 hits.
TIGRFAMsiTIGR02033. D-hydantoinase. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q14195-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MSYQGKKNIP RITSDRLLIK GGRIVNDDQS FYADIYMEDG LIKQIGDNLI
60 70 80 90 100
VPGGVKTIEA NGKMVIPGGI DVHTHFQMPY KGMTTVDDFF QGTKAALAGG
110 120 130 140 150
TTMIIDHVVP EPESSLTEAY EKWREWADGK SCCDYALHVD ITHWNDSVKQ
160 170 180 190 200
EVQNLIKDKG VNSFMVYMAY KDLYQVSNTE LYEIFTCLGE LGAIAQVHAE
210 220 230 240 250
NGDIIAQEQT RMLEMGITGP EGHVLSRPEE LEAEAVFRAI TIASQTNCPL
260 270 280 290 300
YVTKVMSKSA ADLISQARKK GNVVFGEPIT ASLGIDGTHY WSKNWAKAAA
310 320 330 340 350
FVTSPPLSPD PTTPDYINSL LASGDLQLSG SAHCTFSTAQ KAIGKDNFTA
360 370 380 390 400
IPEGTNGVEE RMSVIWDKAV ATGKMDENQF VAVTSTNAAK IFNLYPRKGR
410 420 430 440 450
ISVGSDSDLV IWDPDAVKIV SAKNHQSAAE YNIFEGMELR GAPLVVICQG
460 470 480 490 500
KIMLEDGNLH VTQGAGRFIP CSPFSDYVYK RIKARRKMAD LHAVPRGMYD
510 520 530 540 550
GPVFDLTTTP KGGTPAGSAR GSPTRPNPPV RNLHQSGFSL SGTQVDEGVR
560 570
SASKRIVAPP GGRSNITSLS
Length:570
Mass (Da):61,963
Last modified:November 1, 1996 - v1
Checksum:i9D6AFE86CBB33AD5
GO
Isoform LCRMP-4 (identifier: Q14195-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-13: MSYQGKKNIPRIT → MASGRRGWDS...VLQNLGPKDK

Show »
Length:684
Mass (Da):73,911
Checksum:i1729A3ED4DA83D30
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti49 – 491L → V in CAA69153 (PubMed:9115293).Curated
Sequence conflicti142 – 1421T → A in CAA69153 (PubMed:9115293).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti442 – 4421A → S.
Corresponds to variant rs2304044 [ dbSNP | Ensembl ].
VAR_020485

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 1313MSYQG…IPRIT → MASGRRGWDSSHEDDLPVYL ARPGTTDQVPRQKYGGMFCN VEGAFESKTLDFDALSVGQR GAKTPRSGQGSDRGSGSRPG IEGDTPRRGQGREESREPAP ASPAPAGVEIRSATGKEVLQ NLGPKDK in isoform LCRMP-4. 1 PublicationVSP_042546Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D78014 mRNA. Translation: BAA11192.1.
Y07818 mRNA. Translation: CAA69153.1.
EU007906 mRNA. Translation: ABV80252.1.
AC011373 Genomic DNA. No translation available.
CCDSiCCDS43381.1. [Q14195-1]
CCDS56387.1. [Q14195-2]
PIRiJC5318.
RefSeqiNP_001184223.1. NM_001197294.1. [Q14195-2]
NP_001378.1. NM_001387.2. [Q14195-1]
UniGeneiHs.519659.

Genome annotation databases

EnsembliENST00000343218; ENSP00000343690; ENSG00000113657. [Q14195-2]
ENST00000398514; ENSP00000381526; ENSG00000113657.
GeneIDi1809.
KEGGihsa:1809.
UCSCiuc003lon.1. human. [Q14195-1]
uc003loo.3. human. [Q14195-2]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D78014 mRNA. Translation: BAA11192.1.
Y07818 mRNA. Translation: CAA69153.1.
EU007906 mRNA. Translation: ABV80252.1.
AC011373 Genomic DNA. No translation available.
CCDSiCCDS43381.1. [Q14195-1]
CCDS56387.1. [Q14195-2]
PIRiJC5318.
RefSeqiNP_001184223.1. NM_001197294.1. [Q14195-2]
NP_001378.1. NM_001387.2. [Q14195-1]
UniGeneiHs.519659.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4BKNX-ray2.10A/B1-570[»]
4CNSX-ray2.40A/B/C/D13-490[»]
4CNTX-ray2.65A/B/C/D1-570[»]
4CNUX-ray2.80A/B1-570[»]
ProteinModelPortaliQ14195.
SMRiQ14195. Positions 12-497.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi108143. 30 interactions.
IntActiQ14195. 4 interactions.
STRINGi9606.ENSP00000343690.

Protein family/group databases

MEROPSiM38.976.

PTM databases

PhosphoSiteiQ14195.

Polymorphism and mutation databases

BioMutaiDPYSL3.
DMDMi3122050.

2D gel databases

REPRODUCTION-2DPAGEQ14195.
UCD-2DPAGEQ14195.

Proteomic databases

MaxQBiQ14195.
PaxDbiQ14195.
PRIDEiQ14195.

Protocols and materials databases

DNASUi1809.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000343218; ENSP00000343690; ENSG00000113657. [Q14195-2]
ENST00000398514; ENSP00000381526; ENSG00000113657.
GeneIDi1809.
KEGGihsa:1809.
UCSCiuc003lon.1. human. [Q14195-1]
uc003loo.3. human. [Q14195-2]

Organism-specific databases

CTDi1809.
GeneCardsiGC05M146750.
HGNCiHGNC:3015. DPYSL3.
HPAiHPA010948.
MIMi601168. gene.
neXtProtiNX_Q14195.
PharmGKBiPA27473.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG0044.
GeneTreeiENSGT00760000119241.
HOGENOMiHOG000219145.
HOVERGENiHBG000806.
InParanoidiQ14195.
OMAiGFHLMIS.
OrthoDBiEOG7SJD48.
PhylomeDBiQ14195.
TreeFamiTF314706.

Enzyme and pathway databases

ReactomeiREACT_19199. CRMPs in Sema3A signaling.

Miscellaneous databases

ChiTaRSiDPYSL3. human.
GeneWikiiDPYSL3.
GenomeRNAii1809.
NextBioi7373.
PROiQ14195.
SOURCEiSearch...

Gene expression databases

BgeeiQ14195.
CleanExiHS_DPYSL3.
ExpressionAtlasiQ14195. baseline and differential.
GenevisibleiQ14195. HS.

Family and domain databases

Gene3Di2.30.40.10. 2 hits.
InterProiIPR006680. Amidohydro_1.
IPR030628. DRP3.
IPR011778. Hydantoinase/dihydroPyrase.
IPR011059. Metal-dep_hydrolase_composite.
[Graphical view]
PANTHERiPTHR11647:SF57. PTHR11647:SF57. 1 hit.
PfamiPF01979. Amidohydro_1. 1 hit.
[Graphical view]
SUPFAMiSSF51338. SSF51338. 2 hits.
TIGRFAMsiTIGR02033. D-hydantoinase. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A novel gene family defined by human dihydropyrimidinase and three related proteins with differential tissue distribution."
    Hamajima N., Matsuda K., Sakata S., Tamaki N., Sasaki M., Nonaka M.
    Gene 180:157-163(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    Tissue: Brain.
  2. "Identification and characterization of a retinoic acid-regulated human homologue of the unc-33-like phosphoprotein gene (hUlip) from neuroblastoma cells."
    Gaetano C., Matsuo T., Thiele C.J.
    J. Biol. Chem. 272:12195-12201(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    Tissue: Brain.
  3. "Long form collapsin response mediator protein-1 (LCRMP-1) is a novel invasion enhancer: counter-regulation of cancer cell invasion by LCRMP-1 and CRMP-1."
    Pan S.-H., Hong T.-M., Chao Y.-C., Yang S.-C., Yang P.-C.
    Submitted (JUN-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM LCRMP-4).
  4. "The DNA sequence and comparative analysis of human chromosome 5."
    Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S., Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M., She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S.
    , Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.
    Nature 431:268-274(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. Lubec G., Afjehi-Sadat L., Chen W.-Q., Sun Y.
    Submitted (DEC-2008) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 24-56; 82-122; 131-157; 239-254; 259-268; 346-368; 375-397; 401-418; 424-440; 452-480; 488-511 AND 532-550, IDENTIFICATION BY MASS SPECTROMETRY.
    Tissue: Brain, Cajal-Retzius cell and Fetal brain cortex.
  6. "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
    Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
    Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-102 (ISOFORM LCRMP-4), IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  7. "Distinct priming kinases contribute to differential regulation of collapsin response mediator proteins by glycogen synthase kinase-3 in vivo."
    Cole A.R., Causeret F., Yadirgi G., Hastie C.J., McLauchlan H., McManus E.J., Hernandez F., Eickholt B.J., Nikolic M., Sutherland C.
    J. Biol. Chem. 281:16591-16598(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-522 BY DYRK2, PHOSPHORYLATION AT THR-509; THR-514 AND SER-518 BY GSK3.
  8. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-259; THR-509; THR-514 AND SER-522, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-102 (ISOFORM LCRMP-4), IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-509 AND SER-522, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-102 (ISOFORM LCRMP-4), IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.

Entry informationi

Entry nameiDPYL3_HUMAN
AccessioniPrimary (citable) accession number: Q14195
Secondary accession number(s): B3SXQ8, Q93012
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: November 1, 1996
Last modified: July 22, 2015
This is version 148 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Caution

Lacks most of the conserved residues that are essential for binding the metal cofactor and hence for dihydropyrimidinase activity. Its enzyme activity is therefore unsure.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.