P00350 (6PGD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

Gene names

Name:	gnd
Ordered Locus Names:	b2029, JW2011

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	468 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. Ref.11
Catalytic activity	6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH. Ref.11
Pathway	Carbohydrate degradation; pentose phosphate pathway; D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage): step 3/3.
Subunit structure	Homodimer. Ref.11
Sequence similarities	Belongs to the 6-phosphogluconate dehydrogenase family.
Biophysicochemical properties	Kinetic parameters: KM=49 µM for NADP Ref.11 KM=93 µM for 6-phospho-D-gluconate

Ontologies

Keywords
Biological process	Gluconate utilization Pentose shunt
Ligand	NADP
Molecular function	Oxidoreductase
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-phosphate shunt Inferred from direct assay Ref.11. Source: UniProtKB
Molecular_function	NADP binding Inferred from electronic annotation. Source: InterPro phosphogluconate dehydrogenase (decarboxylating) activity Inferred from direct assay Ref.11. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
nadE	P18843	1	EBI-907049,EBI-548960

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 468

468

6-phosphogluconate dehydrogenase, decarboxylating

PRO_0000090037

Regions

Nucleotide binding

10 – 15

6

NADP

Nucleotide binding

33 – 35

3

NADP

Nucleotide binding

74 – 76

3

NADP

Region

128 – 130

3

Substrate binding

Region

186 – 187

2

Substrate binding By similarity

Sites

Active site

183

1

Proton acceptor Ref.11

Active site

190

1

Proton donor Ref.11

Binding site

102

1

NADP By similarity

Binding site

102

1

Substrate

Binding site

191

1

Substrate By similarity

Binding site

260

1

Substrate; via amide nitrogen

Binding site

287

1

Substrate

Binding site

445

1

Substrate; shared with dimeric partner

Binding site

451

1

Substrate; shared with dimeric partner

Natural variations

Natural variant

2

1

S → L in strain: ECOR 70.

Natural variant

32

1

F → Y in strain: ECOR 70.

Natural variant

39

1

T → Q in strain: O7:K1 / VW187.

Natural variant

52

1

V → D in strain: ECOR 10.

Natural variant

55

1

Y → F in strain: ECOR 10.

Natural variant

102

1

N → K in strain: ECOR 65.

Natural variant

117

1

A → S in strain: ECOR 70.

Natural variant

123 – 125

3

IGT → YRY in strain: O7:K1 / VW187.

Natural variant

170

1

V → F in strain: ECOR 10.

Natural variant

175

1

A → S in strain: ECOR 45.

Natural variant

209

1

N → S in strain: ECOR 68.

Natural variant

211

1

T → S in strain: ECOR 10 and ECOR 69.

Natural variant

216

1

A → T in strain: ECOR 67.

Natural variant

294

1

D → E in strain: ECOR 70.

Natural variant

308

1

A → G in strain: ECOR 68.

Natural variant

313

1

D → N in strain: ECOR 67.

Natural variant

315

1

A → G in strain: ECOR 70.

Natural variant

325

1

L → Q in strain: ECOR 69.

Natural variant

330

1

I → S in strain: ECOR 10.

Natural variant

350

1

D → A in strain: ECOR 10 and ECOR 69.

Natural variant

369

1

Q → R in strain: ECOR 10.

Natural variant

422

1

S → A in strain: ECOR 10, ECOR 65, ECOR 68, ECOR 69 and ECOR 70.

Experimental info

Sequence conflict

306

1

P → R in AAA23918. Ref.1

Secondary structure

1

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468

Helix Strand Turn

Details...

Beta strand

4 – 9

6

Helix

13 – 23

11

Turn

24 – 26

3

Beta strand

29 – 32

4

Helix

36 – 45

10

Beta strand

51 – 53

3

Helix

57 – 62

6

Beta strand

69 – 72

4

Beta strand

76 – 78

3

Helix

79 – 87

9

Helix

88 – 90

3

Beta strand

96 – 99

4

Helix

105 – 117

13

Beta strand

121 – 129

9

Helix

130 – 136

7

Beta strand

139 – 144

6

Helix

146 – 159

14

Beta strand

168 – 170

3

Helix

178 – 208

31

Helix

212 – 224

13

Turn

225 – 227

3

Helix

230 – 240

11

Beta strand

246 – 248

3

Helix

249 – 252

4

Helix

265 – 273

9

Helix

278 – 290

13

Helix

293 – 300

8

Helix

314 – 347

34

Helix

353 – 359

7

Beta strand

361 – 364

4

Helix

370 – 380

11

Helix

387 – 389

3

Helix

391 – 414

24

Helix

419 – 431

13

Helix

438 – 449

12

Beta strand

455 – 458

4

Beta strand

460 – 462

3

Sequences

	Sequence		Length	Mass (Da)
	P00350 [UniParc]. Last modified November 1, 1997. Version 2. Checksum: 62A32C84DC596D86	FASTA	468	51,481
	10 20 30 40 50 60 MSKQQIGVVG MAVMGRNLAL NIESRGYTVS IFNRSREKTE EVIAENPGKK LVPYYTVKEF 70 80 90 100 110 120 VESLETPRRI LLMVKAGAGT DAAIDSLKPY LDKGDIIIDG GNTFFQDTIR RNRELSAEGF 130 140 150 160 170 180 NFIGTGVSGG EEGALKGPSI MPGGQKEAYE LVAPILTKIA AVAEDGEPCV TYIGADGAGH 190 200 210 220 230 240 YVKMVHNGIE YGDMQLIAEA YSLLKGGLNL TNEELAQTFT EWNNGELSSY LIDITKDIFT 250 260 270 280 290 300 KKDEDGNYLV DVILDEAANK GTGKWTSQSA LDLGEPLSLI TESVFARYIS SLKDQRVAAS 310 320 330 340 350 360 KVLSGPQAQP AGDKAEFIEK VRRALYLGKI VSYAQGFSQL RAASEEYNWD LNYGEIAKIF 370 380 390 400 410 420 RAGCIIRAQF LQKITDAYAE NPQIANLLLA PYFKQIADDY QQALRDVVAY AVQNGIPVPT 430 440 450 460 FSAAVAYYDS YRAAVLPANL IQAQRDYFGA HTYKRIDKEG VFHTEWLD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"DNA sequence of the Escherichia coli gene, gnd, for 6-phosphogluconate dehydrogenase." Nasoff M.S., Baker H.V. II, Wolf R.E. Jr. Gene 27:253-264(1984) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Nucleotide sequences of the gnd genes from nine natural isolates of Escherichia coli: evidence of intragenic recombination as a contributing factor in the evolution of the polymorphic gnd locus." Bisercic M., Feutrier J.Y., Reeves P.R. J. Bacteriol. 173:3894-3900(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ECOR 10.
[3]	"Recombination in Escherichia coli and the definition of biological species." Dykhuizen D.E., Green L. J. Bacteriol. 173:7257-7268(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ECOR 45, ECOR 65, ECOR 67, ECOR 68, ECOR 69 and ECOR 70.
[4]	"A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map." Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S. , Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y., Horiuchi T. DNA Res. 3:379-392(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[6]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"Fitness effects of a deletion mutation increasing transcription of the 6-phosphogluconate dehydrogenase gene in Escherichia coli." Miller R.D., Dykhuizen D.E., Hartl D.L. Mol. Biol. Evol. 5:691-703(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-125.
[8]	"Comparative nucleotide sequence analysis of growth-rate-regulated gnd alleles from natural isolates of Escherichia coli and from Salmonella typhimurium LT-2." Barcak G.J., Wolf R.E. Jr. J. Bacteriol. 170:372-379(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-125.
[9]	"Identification, expression, and DNA sequence of the GDP-mannose biosynthesis genes encoded by the O7 rfb gene cluster of strain VW187 (Escherichia coli O7:K1)." Marolda C.L., Valvano M.A. J. Bacteriol. 175:148-158(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-125. Strain: O7:K1 / VW187.
[10]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[11]	"Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: Implications for enzyme mechanism." Chen Y.Y., Ko T.P., Chen W.H., Lo L.P., Lin C.H., Wang A.H. J. Struct. Biol. 169:25-35(2010) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEXES WITH NADP AND SUBSTRATE, SUBUNIT, CATALYTIC ACTIVITY, FUNCTION, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

K02072 Genomic DNA. Translation: AAA23918.1.
M63821 Genomic DNA. Translation: AAA24488.1.
M64326 Genomic DNA. Translation: AAA24204.1.
M64327 Genomic DNA. Translation: AAA24205.1.
M64328 Genomic DNA. Translation: AAA24206.1.
M64329 Genomic DNA. Translation: AAA24207.1.
M64330 Genomic DNA. Translation: AAA24208.1.
M64331 Genomic DNA. Translation: AAA24209.1.
U00096 Genomic DNA. Translation: AAC75090.1.
AP009048 Genomic DNA. Translation: BAA15869.1.
M23181 Genomic DNA. Translation: AAA23924.1.
M18956 Genomic DNA. Translation: AAA23919.1.
M18957 Genomic DNA. Translation: AAA23920.1.
M18960 Genomic DNA. Translation: AAA23922.1.
AF125322 Genomic DNA. Translation: AAC27540.1.

PIR

DEECGC. D64968.
I62463.
I62465.

RefSeq

NP_416533.1. NC_000913.2.
YP_490272.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2ZYA	X-ray	1.60	A/B	1-468	[»]
2ZYD	X-ray	1.50	A/B	1-468	[»]
3FWN	X-ray	1.50	A/B	1-468	[»]

ProteinModelPortal

P00350.

SMR

P00350. Positions 2-467.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9819N.

IntAct

P00350. 5 interactions.

Proteomic databases

PRIDE

P00350.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75090; AAC75090; b2029.
BAA15869; BAA15869; BAA15869.

GeneID

12932360.
946554.

KEGG

ecj:Y75_p1992.
eco:b2029.

PATRIC

32119393. VBIEscCol129921_2106.

Organism-specific databases

EchoBASE

EB0406.

EcoGene

EG10411. gnd.

Phylogenomic databases

KO

K00033.

OMA

KQQIGVI.

ProtClustDB

PRK09287.

Enzyme and pathway databases

BioCyc

EcoCyc:6PGLUCONDEHYDROG-MONOMER.
ECOL316407:JW2011-MONOMER.
MetaCyc:6PGLUCONDEHYDROG-MONOMER.

UniPathway

UPA00115; UER00410.

Gene expression databases

Genevestigator

P00350.

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

EvolutionaryTrace

P00350.

Entry information

Entry name

6PGD_ECOLI

Accession

Primary (citable) accession number: P00350
Secondary accession number(s): P78080 , Q47571, Q59366, Q59402, Q59411, Q59412, Q59413, Q59414, Q59416, Q79DT3

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	November 1, 1997
Last modified:	May 1, 2013
This is version 119 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program