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

Names and origin

Protein names

Recommended name:
6-phosphogluconate dehydrogenase, decarboxylating
EC=1.1.1.44

Gene names

Name:	PGD
Synonyms:	PGDH

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	483 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	Gluconate utilization Pentose shunt
Cellular component	Cytoplasm
Coding sequence diversity	Polymorphism
Ligand	NADP
Molecular function	Oxidoreductase
PTM	Acetylation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	D-gluconate metabolic process Inferred from electronic annotation. Source: UniProtKB-KW pentose biosynthetic process Inferred from electronic annotation. Source: Compara pentose-phosphate shunt, oxidative branch Inferred from direct assay PubMed 3858849. Source: UniProtKB
Cellular_component	cytosol Traceable author statement. Source: Reactome
Molecular_function	NADP binding Inferred from electronic annotation. Source: InterPro phosphogluconate dehydrogenase (decarboxylating) activity Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
NAA38	O95777	1	EBI-372761,EBI-347779

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 483

483

6-phosphogluconate dehydrogenase, decarboxylating

PRO_0000090063

Regions

Nucleotide binding

10 – 15

6

NADP

Nucleotide binding

33 – 35

3

NADP

Nucleotide binding

75 – 77

3

NADP

Nucleotide binding

478 – 481

4

NADP; shared with dimeric partner

Region

129 – 131

3

Substrate binding By similarity

Region

187 – 188

2

Substrate binding By similarity

Sites

Active site

184

1

Proton acceptor By similarity

Active site

191

1

Proton donor By similarity

Binding site

103

1

NADP

Binding site

103

1

Substrate By similarity

Binding site

192

1

Substrate By similarity

Binding site

261

1

Substrate; via amide nitrogen By similarity

Binding site

288

1

Substrate By similarity

Binding site

447

1

Substrate; shared with dimeric partner By similarity

Binding site

453

1

Substrate; shared with dimeric partner By similarity

Amino acid modifications

Modified residue

59

1

N6-acetyllysine Ref.6

Modified residue

309

1

N6-acetyllysine Ref.6

Natural variations

Natural variant

268

1

A → S.
Corresponds to variant rs11547610 [ dbSNP | Ensembl ].

VAR_048104

Experimental info

Sequence conflict

118

1

A → G in AAA75302. Ref.1

Sequence conflict

135

1

A → P in AAA75302. Ref.1

Secondary structure

1

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483

Helix Strand Turn

Details...

Beta strand

4 – 9

6

Helix

13 – 24

12

Beta strand

29 – 32

4

Helix

37 – 44

8

Turn

45 – 49

5

Helix

58 – 63

6

Beta strand

70 – 73

4

Helix

79 – 88

10

Helix

89 – 91

3

Beta strand

97 – 100

4

Helix

106 – 118

13

Beta strand

122 – 130

9

Helix

131 – 137

7

Beta strand

140 – 145

6

Helix

147 – 149

3

Helix

150 – 160

11

Turn

165 – 167

3

Beta strand

169 – 171

3

Helix

179 – 207

29

Helix

213 – 223

11

Turn

224 – 228

5

Helix

231 – 241

11

Beta strand

247 – 250

4

Helix

251 – 253

3

Helix

265 – 274

10

Helix

279 – 292

14

Helix

294 – 301

8

Helix

316 – 349

34

Helix

355 – 361

7

Helix

371 – 382

12

Helix

389 – 391

3

Helix

393 – 416

24

Helix

421 – 433

13

Helix

440 – 451

12

Beta strand

455 – 457

3

Beta strand

460 – 465

6

Sequences

	Sequence		Length	Mass (Da)
	P52209 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 6CEFC0077D1283E3	FASTA	483	53,140
	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

References

	« Hide 'large scale' referencesShow '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. , 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. , 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. , 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, MASS SPECTROMETRY.
[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.

IPI

IPI00219525.

PIR

G01922.

RefSeq

NP_002622.2. NM_002631.2.

UniGene

Hs.464071.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2JKV	X-ray	2.53	A/B/C/D/E/F	1-483	[»]
4GWG	X-ray	1.39	A	2-483	[»]
4GWK	X-ray	1.53	A	2-483	[»]

ProteinModelPortal

P52209.

ModBase

Search...

Protein-protein interaction databases

IntAct

P52209. 6 interactions.

MINT

MINT-1415782.

STRING

9606.ENSP00000270776.

PTM databases

PhosphoSite

P52209.

Polymorphism databases

DMDM

20981679.

Proteomic databases

PaxDb

P52209.

PeptideAtlas

P52209.

PRIDE

P52209.

Protocols and materials databases

DNASU

5226.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000270776; ENSP00000270776; ENSG00000142657.

GeneID

5226.

KEGG

hsa:5226.

UCSC

uc001arc.3. human.

Organism-specific databases

CTD

5226.

GeneCards

GC01P010458.

HGNC

HGNC:8891. PGD.

HPA

HPA031314.

MIM

172200. gene.

neXtProt

NX_P52209.

PharmGKB

PA33229.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG0362.

HOGENOM

HOG000255147.

HOVERGEN

HBG000029.

InParanoid

P52209.

KO

K00033.

OMA

KQQIGVI.

OrthoDB

EOG4C2H9D.

PhylomeDB

P52209.

Enzyme and pathway databases

Reactome

REACT_111217. Metabolism.

SABIO-RK

P52209.

UniPathway

UPA00115; UER00410.

Gene expression databases

ArrayExpress

P52209.

Bgee

P52209.

CleanEx

HS_PGD.

Genevestigator

P52209.

GermOnline

ENSG00000142657. Homo sapiens.

Family and domain databases

Gene3D

1.10.1040.10. 1 hit.
1.20.5.320. 1 hit.
3.40.50.720. 1 hit.

InterPro

IPR008927. 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]

Pfam

PF00393. 6PGD. 1 hit.
PF03446. NAD_binding_2. 1 hit.
[Graphical view]

PIRSF

PIRSF000109. 6PGD. 1 hit.

SUPFAM

SSF48179. 6DGDH_C_like. 1 hit.

TIGRFAMs

TIGR00873. gnd. 1 hit.

PROSITE

PS00461. 6PGD. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

P52209.

ChEMBL

CHEMBL3404.

ChiTaRS

PGD. human.

EvolutionaryTrace

P52209.

GenomeRNAi

5226.

NextBio

20204.

SOURCE

Search...

Entry information

Entry name

6PGD_HUMAN

Accession

Primary (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:	May 1, 2013
This is version 133 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.