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Protein

GDP-mannose 4,6 dehydratase

Gene

Gmd

Organism
Drosophila melanogaster (Fruit fly)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose.1 Publication

Catalytic activityi

GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H2O.

Cofactori

NADP+1 Publication

pH dependencei

Optimum pH is 5-8.1 Publication

Temperature dependencei

Optimum temperature is 30 degrees Celsius.1 Publication

Pathwayi: GDP-L-fucose biosynthesis via de novo pathway

This protein is involved in step 1 of the subpathway that synthesizes GDP-L-fucose from GDP-alpha-D-mannose.1 Publication
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. GDP-mannose 4,6 dehydratase (Gmd)
  2. Probable GDP-L-fucose synthase (Gmer)
This subpathway is part of the pathway GDP-L-fucose biosynthesis via de novo pathway, which is itself part of Nucleotide-sugar biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes GDP-L-fucose from GDP-alpha-D-mannose, the pathway GDP-L-fucose biosynthesis via de novo pathway and in Nucleotide-sugar biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei146 – 1461NADPBy similarity
Active sitei178 – 1781By similarity
Active sitei180 – 1801NucleophileBy similarity
Active sitei202 – 2021NucleophileBy similarity
Binding sitei206 – 2061NADPBy similarity
Binding sitei232 – 2321NADPBy similarity
Binding sitei237 – 2371NADPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi53 – 586NADPBy similarity
Nucleotide bindingi109 – 1102NADPBy similarity
Nucleotide bindingi131 – 1355NADPBy similarity

GO - Molecular functioni

  • GDP-mannose 4,6-dehydratase activity Source: FlyBase

GO - Biological processi

  • 'de novo' GDP-L-fucose biosynthetic process Source: UniProtKB-UniPathway
  • GDP-L-fucose biosynthetic process Source: FlyBase
  • GDP-mannose metabolic process Source: InterPro
  • Notch signaling pathway Source: FlyBase
  • oogenesis Source: FlyBase
  • regulation of stem cell division Source: FlyBase
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

NADP

Enzyme and pathway databases

ReactomeiR-DME-6787639. GDP-fucose biosynthesis.
UniPathwayiUPA00128; UER00190.

Names & Taxonomyi

Protein namesi
Recommended name:
GDP-mannose 4,6 dehydratase (EC:4.2.1.47)
Alternative name(s):
GDP-D-mannose dehydratase
Short name:
Dm-gmd
Gene namesi
Name:Gmd
ORF Names:CG8890
OrganismiDrosophila melanogaster (Fruit fly)
Taxonomic identifieri7227 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraEndopterygotaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
Proteomesi
  • UP000000803 Componenti: Chromosome 2L

Organism-specific databases

FlyBaseiFBgn0031661. Gmd.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 395395GDP-mannose 4,6 dehydratasePRO_0000201707Add
BLAST

Proteomic databases

PaxDbiQ9VMW9.

Expressioni

Gene expression databases

BgeeiQ9VMW9.
ExpressionAtlasiQ9VMW9. differential.
GenevisibleiQ9VMW9. DM.

Interactioni

Protein-protein interaction databases

BioGridi59900. 1 interaction.
STRINGi7227.FBpp0078685.

Structurei

3D structure databases

ProteinModelPortaliQ9VMW9.
SMRiQ9VMW9. Positions 48-392.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1372. Eukaryota.
COG1089. LUCA.
GeneTreeiENSGT00440000033640.
InParanoidiQ9VMW9.
KOiK01711.
OMAiSDMMKAD.
OrthoDBiEOG7K6PV5.
PhylomeDBiQ9VMW9.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00955. GDP_Man_dehydratase.
InterProiIPR006368. GDP_Man_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF16363. GDP_Man_Dehyd. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01472. gmd. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9VMW9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLNTRLIAMS TSDGAPETKK QRPESSSNGS KDQNGTEAGA EGDSRDKVAL
60 70 80 90 100
ITGITGQDGS YLAEFLLKKD YEVHGIIRRA STFNTTRIEH LYADPKAHKG
110 120 130 140 150
GRMKLHYGDM TDSSSLVKII NMVKPTEIYN LAAQSHVKVS FDLSEYTAEV
160 170 180 190 200
DAVGTLRILD AIRTCGMEKN VRFYQASTSE LYGKVVETPQ NEQTPFYPRS
210 220 230 240 250
PYACAKMYGF WIVINYREAY NMYACNGILF NHESPRRGEN FVTRKITRSV
260 270 280 290 300
AKIYHKQMEY FELGNLDSKR DWGHASDYVE AMWMMLQRES PSDYVIATGE
310 320 330 340 350
THSVREFVEA AFKHIDREIT WKGKGVDEVG VENGTGIVRV RINPKYFRPT
360 370 380 390
EVDLLQGDAS KANRELNWTP KVTFVELVSD MMKADIELMR KNPIA
Length:395
Mass (Da):44,784
Last modified:July 25, 2003 - v2
Checksum:i533E1B41E69ED36D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti333 – 3331N → S in CAJ77750 (PubMed:16650000).Curated
Sequence conflicti333 – 3331N → S in AAL90257 (PubMed:12537569).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM231687 mRNA. Translation: CAJ77750.1.
AE014134 Genomic DNA. Translation: AAF52189.2.
AY089519 mRNA. Translation: AAL90257.1.
RefSeqiNP_608888.2. NM_135044.4.
UniGeneiDm.4967.

Genome annotation databases

EnsemblMetazoaiFBtr0079049; FBpp0078685; FBgn0031661.
GeneIDi33716.
KEGGidme:Dmel_CG8890.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM231687 mRNA. Translation: CAJ77750.1.
AE014134 Genomic DNA. Translation: AAF52189.2.
AY089519 mRNA. Translation: AAL90257.1.
RefSeqiNP_608888.2. NM_135044.4.
UniGeneiDm.4967.

3D structure databases

ProteinModelPortaliQ9VMW9.
SMRiQ9VMW9. Positions 48-392.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi59900. 1 interaction.
STRINGi7227.FBpp0078685.

Proteomic databases

PaxDbiQ9VMW9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiFBtr0079049; FBpp0078685; FBgn0031661.
GeneIDi33716.
KEGGidme:Dmel_CG8890.

Organism-specific databases

CTDi33716.
FlyBaseiFBgn0031661. Gmd.

Phylogenomic databases

eggNOGiKOG1372. Eukaryota.
COG1089. LUCA.
GeneTreeiENSGT00440000033640.
InParanoidiQ9VMW9.
KOiK01711.
OMAiSDMMKAD.
OrthoDBiEOG7K6PV5.
PhylomeDBiQ9VMW9.

Enzyme and pathway databases

UniPathwayiUPA00128; UER00190.
ReactomeiR-DME-6787639. GDP-fucose biosynthesis.

Miscellaneous databases

GenomeRNAii33716.
NextBioi784930.
PROiQ9VMW9.

Gene expression databases

BgeeiQ9VMW9.
ExpressionAtlasiQ9VMW9. differential.
GenevisibleiQ9VMW9. DM.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00955. GDP_Man_dehydratase.
InterProiIPR006368. GDP_Man_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF16363. GDP_Man_Dehyd. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01472. gmd. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Reconstitution in vitro of the GDP-fucose biosynthetic pathways of Caenorhabditis elegans and Drosophila melanogaster."
    Rhomberg S., Fuchsluger C., Rendic D., Paschinger K., Jantsch V., Kosma P., Wilson I.B.H.
    FEBS J. 273:2244-2256(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, COFACTOR, PATHWAY, BIOPHYSICOCHEMICAL PROPERTIES.
  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. Cited for: GENOME REANNOTATION.
    Strain: Berkeley.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: Berkeley.
    Tissue: Ovary.
  5. "Composition of Drosophila melanogaster proteome involved in fucosylated glycan metabolism."
    Roos C., Kolmer M., Mattila P., Renkonen R.
    J. Biol. Chem. 277:3168-3175(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: HOMOLOGY.

Entry informationi

Entry nameiGMDS_DROME
AccessioniPrimary (citable) accession number: Q9VMW9
Secondary accession number(s): Q1H8X2, Q8T3U5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: July 25, 2003
Last modified: February 17, 2016
This is version 117 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programDrosophila annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Drosophila
    Drosophila: entries, gene names and cross-references to FlyBase
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.