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

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) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	468 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

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.
Sequence similarities	Belongs to the 6-phosphogluconate dehydrogenase family.

Ontologies

Keywords
Biological process	Gluconate utilization Pentose shunt
Ligand	NADP
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	D-gluconate metabolic process Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW pentose-phosphate shunt Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	NADP or NADPH binding Inferred from electronic annotation. Source: InterPro phosphogluconate dehydrogenase (decarboxylating) activity Inferred from mutant phenotype. Source: UniProtKB protein binding Inferred from physical interaction. Source: IntAct
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

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

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468

Helix Strand Turn

Details...

Helix

17 – 23

7

Beta strand

29 – 31

3

Helix

36 – 45

10

Beta strand

51 – 53

3

Helix

57 – 62

6

Beta strand

69 – 72

4

Helix

81 – 87

7

Helix

88 – 90

3

Beta strand

96 – 98

3

Helix

105 – 117

13

Beta strand

121 – 123

3

Helix

146 – 159

14

Beta strand

168 – 170

3

Helix

181 – 186

6

Helix

194 – 204

11

Helix

212 – 223

12

Helix

230 – 240

11

Helix

249 – 252

4

Helix

265 – 272

8

Helix

278 – 290

13

Helix

293 – 300

8

Helix

314 – 326

13

Helix

330 – 334

5

Helix

338 – 347

10

Helix

356 – 359

4

Helix

370 – 380

11

Helix

387 – 389

3

Helix

391 – 413

23

Helix

419 – 431

13

Helix

438 – 447

10

Beta strand

455 – 457

3

Sequences

	Sequence		Length	Mass (Da)
	P00350-1 [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: 6329905] [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: 2050640] [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: 1938920] [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: 9097040] [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: 9278503] [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: 16738553] [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: 2464736] [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: 3275621] [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: 7677991] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-125. Strain: O7:K1 / VW187.
+	Additional computationally mapped references.

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

AP_002630.1.
NP_416533.1.

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	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P00350. 5 interactions.

2-D gel databases

ECO2DBASE

C042.6. 6TH EDITION.

Proteomic databases

PRIDE

P00350.

Genome annotation databases

GeneID

946554.

GenomeReviews

Gene locus JW2011 in contig AP009048_GR.
Gene locus b2029 in contig U00096_GR.

KEGG

ecj:JW2011.
eco:b2029.

Organism-specific databases

EchoBASE

EB0406.

EcoGene

EG10411. gnd.

CMR

Search...

Phylogenomic databases

OMA

GQKEAYD.

Enzyme and pathway databases

BioCyc

EcoCyc:6PGLUCONDEHYDROG-MONOMER.
ECOL168927:B2029-MONOMER.
MetaCyc:6PGLUCONDEHYDROG-MONOMER.

Gene expression databases

Genevestigator

P00350.

Family and domain databases

InterPro

IPR008927. 6-PGluconate_DH_C-like.
IPR006183. 6-phosphogluconate_DH.
IPR006114. 6PGDH_C.
IPR006113. 6PGDH_decarbox.
IPR006115. 6PGDH_NAD-bd.
IPR006184. 6PGdom_BS.
IPR013328. DH_multihelical.
IPR012284. Fibritin/6PGD_C-extension.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

Gene3D

G3DSA:1.20.5.320. Fibritin/6PGD_C-extension. 1 hit.
G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.
G3DSA:1.10.1040.10. Opine_DH. 1 hit.

Pfam

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

PRINTS

PR00076. 6PGDHDRGNASE.

TIGRFAMs

TIGR00873. gnd. 1 hit.

PROSITE

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

ProtoNet

Search...

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:	February 9, 2010
This is version 92 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)