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P52209 (6PGD_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 142. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (7) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
6-phosphogluconate dehydrogenase, decarboxylating

EC=1.1.1.44
Gene names
Name:PGD
Synonyms:PGDH
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length483 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Catalytic activity

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

Pathway

Carbohydrate degradation; pentose phosphate pathway; D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage): step 3/3.

Subunit structure

Homodimer. Ref.8

Subcellular location

Cytoplasm By similarity.

Sequence similarities

Belongs to the 6-phosphogluconate dehydrogenase family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 4834826-phosphogluconate dehydrogenase, decarboxylating
PRO_0000090063

Regions

Nucleotide binding10 – 156NADP
Nucleotide binding33 – 353NADP
Nucleotide binding75 – 773NADP
Nucleotide binding478 – 4814NADP; shared with dimeric partner
Region129 – 1313Substrate binding By similarity
Region187 – 1882Substrate binding By similarity

Sites

Active site1841Proton acceptor By similarity
Active site1911Proton donor By similarity
Binding site1031NADP
Binding site1031Substrate By similarity
Binding site1921Substrate By similarity
Binding site2611Substrate; via amide nitrogen By similarity
Binding site2881Substrate By similarity
Binding site4471Substrate; shared with dimeric partner By similarity
Binding site4531Substrate; shared with dimeric partner By similarity

Amino acid modifications

Modified residue381N6-acetyllysine By similarity
Modified residue591N6-acetyllysine Ref.6
Modified residue2571Phosphoserine By similarity
Modified residue2631Phosphothreonine By similarity
Modified residue2671Phosphothreonine By similarity
Modified residue2701Phosphoserine By similarity
Modified residue3091N6-acetyllysine Ref.6

Natural variations

Natural variant2681A → S.
Corresponds to variant rs11547610 [ dbSNP | Ensembl ].
VAR_048104

Experimental info

Sequence conflict1181A → G in AAA75302. Ref.1
Sequence conflict1351A → P in AAA75302. Ref.1

Secondary structure

................................................................... 483
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P52209 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 6CEFC0077D1283E3

FASTA48353,140
        10         20         30         40         50         60 
MAQADIALIG LAVMGQNLIL NMNDHGFVVC AFNRTVSKVD DFLANEAKGT KVVGAQSLKE 

        70         80         90        100        110        120 
MVSKLKKPRR IILLVKAGQA VDDFIEKLVP LLDTGDIIID GGNSEYRDTT RRCRDLKAKG 

       130        140        150        160        170        180 
ILFVGSGVSG GEEGARYGPS LMPGGNKEAW PHIKTIFQGI AAKVGTGEPC CDWVGDEGAG 

       190        200        210        220        230        240 
HFVKMVHNGI EYGDMQLICE AYHLMKDVLG MAQDEMAQAF EDWNKTELDS FLIEITANIL 

       250        260        270        280        290        300 
KFQDTDGKHL LPKIRDSAGQ KGTGKWTAIS ALEYGVPVTL IGEAVFARCL SSLKDERIQA 

       310        320        330        340        350        360 
SKKLKGPQKF QFDGDKKSFL EDIRKALYAS KIISYAQGFM LLRQAATEFG WTLNYGGIAL 

       370        380        390        400        410        420 
MWRGGCIIRS VFLGKIKDAF DRNPELQNLL LDDFFKSAVE NCQDSWRRAV STGVQAGIPM 

       430        440        450        460        470        480 
PCFTTALSFY DGYRHEMLPA SLIQAQRDYF GAHTYELLAK PGQFIHTNWT GHGGTVSSSS 


YNA 

« Hide

References

« Hide 'large scale' references
[1]"Identification of a cDNA encoding 6-phosphogluconate dehydrogenase from a human heart cDNA library."
Tsui S.K.W., Chan J.Y., Waye M.M.Y., Fung K.-P., Lee C.-Y.
Biochem. Genet. 34:367-373(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
Tissue: Heart.
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Umbilical cord blood.
[3]"The DNA sequence and biological annotation of human chromosome 1."
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. expand/collapse author list , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Lung.
[6]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-59 AND LYS-309, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[7]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]"Structure of human phosphogluconate dehydrogenase in complex with NADPH at 2.53 A."
Structural genomics consortium (SGC)
Submitted (SEP-2009) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (2.53 ANGSTROMS) IN COMPLEX WITH NADP, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U30255 mRNA. Translation: AAA75302.1.
AK290404 mRNA. Translation: BAF83093.1.
AL139424 Genomic DNA. Translation: CAI95751.1.
CH471130 Genomic DNA. Translation: EAW71648.1.
BC000368 mRNA. Translation: AAH00368.1.
PIRG01922.
RefSeqNP_002622.2. NM_002631.2.
UniGeneHs.464071.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2JKVX-ray2.53A/B/C/D/E/F1-483[»]
4GWGX-ray1.39A2-483[»]
4GWKX-ray1.53A2-483[»]
ProteinModelPortalP52209.
SMRP52209. Positions 2-470.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid111247. 33 interactions.
IntActP52209. 6 interactions.
MINTMINT-1415782.
STRING9606.ENSP00000270776.

Chemistry

BindingDBP52209.
ChEMBLCHEMBL3404.

PTM databases

PhosphoSiteP52209.

Polymorphism databases

DMDM20981679.

Proteomic databases

PaxDbP52209.
PeptideAtlasP52209.
PRIDEP52209.

Protocols and materials databases

DNASU5226.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000270776; ENSP00000270776; ENSG00000142657.
GeneID5226.
KEGGhsa:5226.
UCSCuc001arc.3. human.

Organism-specific databases

CTD5226.
GeneCardsGC01P010458.
HGNCHGNC:8891. PGD.
HPAHPA031314.
MIM172200. gene.
neXtProtNX_P52209.
PharmGKBPA33229.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0362.
HOGENOMHOG000255147.
HOVERGENHBG000029.
InParanoidP52209.
KOK00033.
OMAKQQIGVI.
PhylomeDBP52209.
TreeFamTF300386.

Enzyme and pathway databases

ReactomeREACT_111217. Metabolism.
SABIO-RKP52209.
UniPathwayUPA00115; UER00410.

Gene expression databases

ArrayExpressP52209.
BgeeP52209.
CleanExHS_PGD.
GenevestigatorP52209.

Family and domain databases

Gene3D1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.
InterProIPR008927. 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]
PfamPF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]
PIRSFPIRSF000109. 6PGD. 1 hit.
SUPFAMSSF48179. SSF48179. 1 hit.
TIGRFAMsTIGR00873. gnd. 1 hit.
PROSITEPS00461. 6PGD. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSPGD. human.
EvolutionaryTraceP52209.
GenomeRNAi5226.
NextBio20204.
PROP52209.
SOURCESearch...

Entry information

Entry name6PGD_HUMAN
AccessionPrimary (citable) accession number: P52209
Secondary accession number(s): A8K2Y9, Q9BWD8
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 142 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM