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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

gnd

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO2, with concomitant reduction of NADP to NADPH.By similarity

Catalytic activityi

6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH.

Pathway: pentose phosphate pathway

This protein is involved in step 3 of the subpathway that synthesizes D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage).
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. Glucose-6-phosphate 1-dehydrogenase (g6pd-1)
  2. Probable 6-phosphogluconolactonase (pgl)
  3. 6-phosphogluconate dehydrogenase, decarboxylating (gnd)
This subpathway is part of the pathway pentose phosphate pathway, which is itself part of Carbohydrate degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage), the pathway pentose phosphate pathway and in Carbohydrate degradation.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei105 – 1051NADPBy similarity
Binding sitei105 – 1051SubstrateBy similarity
Active sitei187 – 1871Proton acceptorBy similarity
Active sitei194 – 1941Proton donorBy similarity
Binding sitei195 – 1951SubstrateBy similarity
Binding sitei266 – 2661Substrate; via amide nitrogenBy similarity
Binding sitei293 – 2931SubstrateBy similarity
Binding sitei456 – 4561Substrate; shared with dimeric partnerBy similarity
Binding sitei462 – 4621Substrate; shared with dimeric partnerBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi12 – 176NADPBy similarity
Nucleotide bindingi35 – 373NADPBy similarity
Nucleotide bindingi77 – 793NADPBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Gluconate utilization, Pentose shunt

Keywords - Ligandi

NADP

Enzyme and pathway databases

ReactomeiREACT_354547. Pentose phosphate pathway (hexose monophosphate shunt).
UniPathwayiUPA00115; UER00410.

Names & Taxonomyi

Protein namesi
Recommended name:
6-phosphogluconate dehydrogenase, decarboxylating (EC:1.1.1.44)
Gene namesi
Name:gnd
Synonyms:PGD
ORF Names:DDB_G0277885
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
ProteomesiUP000002195 Componentsi: Chromosome 3, Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0277885. gnd.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 4934936-phosphogluconate dehydrogenase, decarboxylatingPRO_0000327487Add
BLAST

Proteomic databases

PRIDEiQ8TA03.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi44689.DDB0215011.

Structurei

3D structure databases

ProteinModelPortaliQ8TA03.
SMRiQ8TA03. Positions 4-484.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni131 – 1333Substrate bindingBy similarity
Regioni190 – 1912Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0362.
InParanoidiQ8TA03.
KOiK00033.
OMAiSEAYFIL.
PhylomeDBiQ8TA03.

Family and domain databases

Gene3Di1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.
InterProiIPR008927. 6-PGluconate_DH_C-like.
IPR013328. 6PGD_dom_2.
IPR012284. 6PGD_dom_3.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_Gnd/GntZ.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR016040. NAD(P)-bd_dom.
IPR006183. Pgluconate_DH.
[Graphical view]
PfamiPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000109. 6PGD. 1 hit.
PRINTSiPR00076. 6PGDHDRGNASE.
SUPFAMiSSF48179. SSF48179. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8TA03-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTEAKGDIGL IGLAVMGENL VLNMESRGFT CSVYNRTTSK VDEFVQGRGK
60 70 80 90 100
GKKFIGCHSL ETLVQSLKTP RRVMLMVKAG EVVDHFIQLL LPLLEKGDII
110 120 130 140 150
IDGGNSLYTD SDRRTKDLDA KGILFIGTGV SGGEEGALLG PSIMPGGNPK
160 170 180 190 200
AWEHVKPIFQ AISAKVQPGD QPCCDWVGDG GAGHYVKMVH NGIEYGDMQL
210 220 230 240 250
ISEAYFILKH YLGLSNDELQ KTFAKWNTGD LDSYLIEITA DIFAKKCEKD
260 270 280 290 300
PNTYVVDTIL DSAGQKGTGK WTAINALDVG IPLTLVAESV FARCVSSFKE
310 320 330 340 350
ERVKASTILA GPNPNEANKK FTGDKEQVIE AVRQALFASK LVSYAQGFTM
360 370 380 390 400
MKAAAKEYKW NLNYGNIALL WRGGCIIRST FLGEIKGAFD KNPQLDNLLT
410 420 430 440 450
DCWFRDKLAA AQDGWRQVAS ISVLHGIPTP AFTSALSYYD SYRCAKLSAN
460 470 480 490
LVQAQRDYFG AHTFQLLDDP KGAPVHVNWT GRGGSTHSTT YSI
Length:493
Mass (Da):53,891
Last modified:June 1, 2002 - v1
Checksum:iC3FD8A0F07DFC688
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF394516 Genomic DNA. Translation: AAL76326.1.
AAFI02000023 Genomic DNA. Translation: EAL68115.1.
RefSeqiXP_642122.1. XM_637030.1.

Genome annotation databases

EnsemblProtistsiDDB0215011; DDB0215011; DDB_G0277885.
GeneIDi8621331.
KEGGiddi:DDB_G0277885.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF394516 Genomic DNA. Translation: AAL76326.1.
AAFI02000023 Genomic DNA. Translation: EAL68115.1.
RefSeqiXP_642122.1. XM_637030.1.

3D structure databases

ProteinModelPortaliQ8TA03.
SMRiQ8TA03. Positions 4-484.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi44689.DDB0215011.

Proteomic databases

PRIDEiQ8TA03.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsiDDB0215011; DDB0215011; DDB_G0277885.
GeneIDi8621331.
KEGGiddi:DDB_G0277885.

Organism-specific databases

dictyBaseiDDB_G0277885. gnd.

Phylogenomic databases

eggNOGiCOG0362.
InParanoidiQ8TA03.
KOiK00033.
OMAiSEAYFIL.
PhylomeDBiQ8TA03.

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.
ReactomeiREACT_354547. Pentose phosphate pathway (hexose monophosphate shunt).

Miscellaneous databases

PROiQ8TA03.

Family and domain databases

Gene3Di1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.
InterProiIPR008927. 6-PGluconate_DH_C-like.
IPR013328. 6PGD_dom_2.
IPR012284. 6PGD_dom_3.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_Gnd/GntZ.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR016040. NAD(P)-bd_dom.
IPR006183. Pgluconate_DH.
[Graphical view]
PfamiPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000109. 6PGD. 1 hit.
PRINTSiPR00076. 6PGDHDRGNASE.
SUPFAMiSSF48179. SSF48179. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A cyanobacterial gene in nonphotosynthetic protists -- an early chloroplast acquisition in eukaryotes?"
    Andersson J.O., Roger A.J.
    Curr. Biol. 12:115-119(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The genome of the social amoeba Dictyostelium discoideum."
    Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
    , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
    Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AX4.
  3. Bienvenut W.V., Veltman D.M., Insall R.H.
    Submitted (JAN-2010) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 37-48; 305-320 AND 447-456, IDENTIFICATION BY MASS SPECTROMETRY.

Entry informationi

Entry namei6PGD_DICDI
AccessioniPrimary (citable) accession number: Q8TA03
Secondary accession number(s): Q54YT0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 8, 2008
Last sequence update: June 1, 2002
Last modified: June 24, 2015
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. 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.