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Protein

6-phosphogluconate dehydrogenase, decarboxylating

Gene

Pgd

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 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.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei103 – 1031NADPBy similarity
Binding sitei103 – 1031SubstrateBy similarity
Active sitei184 – 1841Proton acceptorBy similarity
Active sitei191 – 1911Proton donorBy similarity
Binding sitei192 – 1921SubstrateBy similarity
Binding sitei261 – 2611Substrate; via amide nitrogenBy similarity
Binding sitei288 – 2881SubstrateBy similarity
Binding sitei447 – 4471Substrate; shared with dimeric partnerBy similarity
Binding sitei453 – 4531Substrate; shared with dimeric partnerBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi10 – 156NADPBy similarity
Nucleotide bindingi33 – 353NADPBy similarity
Nucleotide bindingi75 – 773NADPBy similarity
Nucleotide bindingi478 – 4814NADP; shared with dimeric partnerBy similarity

GO - Molecular functioni

  1. NADP binding Source: InterPro
  2. phosphogluconate dehydrogenase (decarboxylating) activity Source: UniProtKB

GO - Biological processi

  1. D-gluconate metabolic process Source: UniProtKB-KW
  2. oxidation-reduction process Source: MGI
  3. pentose biosynthetic process Source: MGI
  4. pentose-phosphate shunt Source: UniProtKB
  5. pentose-phosphate shunt, oxidative branch Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Gluconate utilization, Pentose shunt

Keywords - Ligandi

NADP

Enzyme and pathway databases

ReactomeiREACT_246505. 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:Pgd
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 4

Organism-specific databases

MGIiMGI:97553. Pgd.

Subcellular locationi

Cytoplasm By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
  2. extracellular vesicular exosome Source: MGI
  3. nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 4834826-phosphogluconate dehydrogenase, decarboxylatingPRO_0000090064Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei38 – 381N6-acetyllysine1 Publication
Modified residuei59 – 591N6-acetyllysineBy similarity
Modified residuei257 – 2571PhosphoserineBy similarity
Modified residuei263 – 2631PhosphothreonineBy similarity
Modified residuei267 – 2671PhosphothreonineBy similarity
Modified residuei270 – 2701PhosphoserineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ9DCD0.
PaxDbiQ9DCD0.
PRIDEiQ9DCD0.

PTM databases

PhosphoSiteiQ9DCD0.

Expressioni

Gene expression databases

BgeeiQ9DCD0.
CleanExiMM_PGD.
GenevestigatoriQ9DCD0.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

MINTiMINT-1868998.

Structurei

3D structure databases

ProteinModelPortaliQ9DCD0.
SMRiQ9DCD0. Positions 2-470.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni129 – 1313Substrate bindingBy similarity
Regioni187 – 1882Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0362.
GeneTreeiENSGT00390000009023.
HOGENOMiHOG000255147.
HOVERGENiHBG000029.
InParanoidiQ9DCD0.
KOiK00033.
OMAiAFAFEEW.
OrthoDBiEOG7K3TKV.
PhylomeDBiQ9DCD0.
TreeFamiTF300386.

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.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_decarbox.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR013328. DH_multihelical.
IPR012284. Fibritin/6PGD_C-extension.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000109. 6PGD. 1 hit.
SUPFAMiSSF48179. SSF48179. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9DCD0-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAQADIALIG LAVMGQNLIL NMNDHGFVVC AFNRTVSKVD DFLANEAKGT
60 70 80 90 100
KVVGAQSLKD MVSKLKKPRR VILLVKAGQA VDDFIEKLVP LLDTGDIIID
110 120 130 140 150
GGNSEYRDTT RRCRDLKAKG ILFVGSGVSG GEEGARYGPS LMPGGNKEAW
160 170 180 190 200
PHIKAIFQAI AAKVGTGEPC CDWVGDEGAG HFVKMVHNGI EYGDMQLICE
210 220 230 240 250
AYHLMKDVLG MRHEEMAQAF EEWNKTELDS FLIEITANIL KYRDTDGKEL
260 270 280 290 300
LPKIRDSAGQ KGTGKWTAIS ALEYGMPVTL IGEAVFARCL SSLKEERVQA
310 320 330 340 350
SQKLKGPKVV QLEGSKKSFL EDIRKALYAS KIISYAQGFM LLRQAATEFG
360 370 380 390 400
WTLNYGGIAL MWRGGCIIRS VFLGKIKDAF ERNPELQNLL LDDFFKSAVD
410 420 430 440 450
NCQDSWRRVI STGVQAGIPM PCFTTALSFY DGYRHEMLPA NLIQAQRDYF
460 470 480
GAHTYELLTK PGEFIHTNWT GHGGSVSSSS YNA
Length:483
Mass (Da):53,247
Last modified:January 23, 2007 - v3
Checksum:iCD0A3F72EEC2831E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK002894 mRNA. Translation: BAB22439.1.
AK145602 mRNA. Translation: BAE26535.1.
AK150210 mRNA. Translation: BAE29381.1.
AK153409 mRNA. Translation: BAE31969.1.
AK155027 mRNA. Translation: BAE32999.1.
AK166733 mRNA. Translation: BAE38978.1.
AK166947 mRNA. Translation: BAE39134.1.
AK167215 mRNA. Translation: BAE39341.1.
AK168251 mRNA. Translation: BAE40201.1.
CCDSiCCDS38974.1.
RefSeqiNP_001074743.1. NM_001081274.1.
UniGeneiMm.252080.

Genome annotation databases

EnsembliENSMUST00000084124; ENSMUSP00000081141; ENSMUSG00000028961.
GeneIDi110208.
KEGGimmu:110208.
UCSCiuc008vvv.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK002894 mRNA. Translation: BAB22439.1.
AK145602 mRNA. Translation: BAE26535.1.
AK150210 mRNA. Translation: BAE29381.1.
AK153409 mRNA. Translation: BAE31969.1.
AK155027 mRNA. Translation: BAE32999.1.
AK166733 mRNA. Translation: BAE38978.1.
AK166947 mRNA. Translation: BAE39134.1.
AK167215 mRNA. Translation: BAE39341.1.
AK168251 mRNA. Translation: BAE40201.1.
CCDSiCCDS38974.1.
RefSeqiNP_001074743.1. NM_001081274.1.
UniGeneiMm.252080.

3D structure databases

ProteinModelPortaliQ9DCD0.
SMRiQ9DCD0. Positions 2-470.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

MINTiMINT-1868998.

PTM databases

PhosphoSiteiQ9DCD0.

Proteomic databases

MaxQBiQ9DCD0.
PaxDbiQ9DCD0.
PRIDEiQ9DCD0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000084124; ENSMUSP00000081141; ENSMUSG00000028961.
GeneIDi110208.
KEGGimmu:110208.
UCSCiuc008vvv.1. mouse.

Organism-specific databases

CTDi5226.
MGIiMGI:97553. Pgd.

Phylogenomic databases

eggNOGiCOG0362.
GeneTreeiENSGT00390000009023.
HOGENOMiHOG000255147.
HOVERGENiHBG000029.
InParanoidiQ9DCD0.
KOiK00033.
OMAiAFAFEEW.
OrthoDBiEOG7K3TKV.
PhylomeDBiQ9DCD0.
TreeFamiTF300386.

Enzyme and pathway databases

UniPathwayiUPA00115; UER00410.
ReactomeiREACT_246505. Pentose phosphate pathway (hexose monophosphate shunt).

Miscellaneous databases

ChiTaRSiPgd. mouse.
NextBioi363535.
PROiQ9DCD0.
SOURCEiSearch...

Gene expression databases

BgeeiQ9DCD0.
CleanExiMM_PGD.
GenevestigatoriQ9DCD0.

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.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_decarbox.
IPR006115. 6PGDH_NADP-bd.
IPR006184. 6PGdom_BS.
IPR013328. DH_multihelical.
IPR012284. Fibritin/6PGD_C-extension.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFiPIRSF000109. 6PGD. 1 hit.
SUPFAMiSSF48179. SSF48179. 1 hit.
TIGRFAMsiTIGR00873. gnd. 1 hit.
PROSITEiPS00461. 6PGD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: BALB/c and C57BL/6J.
    Tissue: Bone marrow and Kidney.
  2. "SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
    Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
    Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-38, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Embryonic fibroblast.

Entry informationi

Entry namei6PGD_MOUSE
AccessioniPrimary (citable) accession number: Q9DCD0
Secondary accession number(s): Q3UD80
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 15, 2002
Last sequence update: January 23, 2007
Last modified: February 4, 2015
This is version 118 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  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.