6PGD_ECOLI
ID 6PGD_ECOLI Reviewed; 468 AA.
AC P00350; P78080; Q47571; Q59366; Q59402; Q59411; Q59412; Q59413; Q59414;
AC Q59416; Q79DT3;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 183.
DE RecName: Full=6-phosphogluconate dehydrogenase, decarboxylating;
DE EC=1.1.1.44;
GN Name=gnd; OrderedLocusNames=b2029, JW2011;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6329905; DOI=10.1016/0378-1119(84)90070-2;
RA Nasoff M.S., Baker H.V. II, Wolf R.E. Jr.;
RT "DNA sequence of the Escherichia coli gene, gnd, for 6-phosphogluconate
RT dehydrogenase.";
RL Gene 27:253-264(1984).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ECOR 10;
RX PubMed=2050640; DOI=10.1128/jb.173.12.3894-3900.1991;
RA Bisercic M., Feutrier J.Y., Reeves P.R.;
RT "Nucleotide sequences of the gnd genes from nine natural isolates of
RT Escherichia coli: evidence of intragenic recombination as a contributing
RT factor in the evolution of the polymorphic gnd locus.";
RL J. Bacteriol. 173:3894-3900(1991).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ECOR 45, ECOR 65, ECOR 67, ECOR 68, ECOR 69, and ECOR 70;
RX PubMed=1938920; DOI=10.1128/jb.173.22.7257-7268.1991;
RA Dykhuizen D.E., Green L.;
RT "Recombination in Escherichia coli and the definition of biological
RT species.";
RL J. Bacteriol. 173:7257-7268(1991).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097040; DOI=10.1093/dnares/3.6.379;
RA Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K.,
RA Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T.,
RA Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y.,
RA Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y.,
RA Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y.,
RA Horiuchi T.;
RT "A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 40.1-50.0 min region on the linkage map.";
RL DNA Res. 3:379-392(1996).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-125.
RX PubMed=2464736; DOI=10.1093/oxfordjournals.molbev.a040522;
RA Miller R.D., Dykhuizen D.E., Hartl D.L.;
RT "Fitness effects of a deletion mutation increasing transcription of the 6-
RT phosphogluconate dehydrogenase gene in Escherichia coli.";
RL Mol. Biol. Evol. 5:691-703(1988).
RN [8]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-125.
RX PubMed=3275621; DOI=10.1128/jb.170.1.372-379.1988;
RA Barcak G.J., Wolf R.E. Jr.;
RT "Comparative nucleotide sequence analysis of growth-rate-regulated gnd
RT alleles from natural isolates of Escherichia coli and from Salmonella
RT typhimurium LT-2.";
RL J. Bacteriol. 170:372-379(1988).
RN [9]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-125.
RC STRAIN=O7:K1 / VW187;
RX PubMed=7677991; DOI=10.1128/jb.175.1.148-158.1993;
RA Marolda C.L., Valvano M.A.;
RT "Identification, expression, and DNA sequence of the GDP-mannose
RT biosynthesis genes encoded by the O7 rfb gene cluster of strain VW187
RT (Escherichia coli O7:K1).";
RL J. Bacteriol. 175:148-158(1993).
RN [10]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEXES WITH NADP AND SUBSTRATE,
RP SUBUNIT, CATALYTIC ACTIVITY, FUNCTION, ACTIVE SITE, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND PATHWAY.
RX PubMed=19686854; DOI=10.1016/j.jsb.2009.08.006;
RA Chen Y.Y., Ko T.P., Chen W.H., Lo L.P., Lin C.H., Wang A.H.;
RT "Conformational changes associated with cofactor/substrate binding of 6-
RT phosphogluconate dehydrogenase from Escherichia coli and Klebsiella
RT pneumoniae: Implications for enzyme mechanism.";
RL J. Struct. Biol. 169:25-35(2010).
CC -!- FUNCTION: Catalyzes the oxidative decarboxylation of 6-phosphogluconate
CC to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP
CC to NADPH. {ECO:0000269|PubMed:19686854}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=6-phospho-D-gluconate + NADP(+) = CO2 + D-ribulose 5-phosphate
CC + NADPH; Xref=Rhea:RHEA:10116, ChEBI:CHEBI:16526, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58121, ChEBI:CHEBI:58349, ChEBI:CHEBI:58759; EC=1.1.1.44;
CC Evidence={ECO:0000269|PubMed:19686854};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=49 uM for NADP {ECO:0000269|PubMed:19686854};
CC KM=93 uM for 6-phospho-D-gluconate {ECO:0000269|PubMed:19686854};
CC -!- PATHWAY: Carbohydrate degradation; pentose phosphate pathway; D-
CC ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage): step
CC 3/3. {ECO:0000305|PubMed:19686854}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:19686854}.
CC -!- INTERACTION:
CC P00350; P00350: gnd; NbExp=4; IntAct=EBI-907049, EBI-907049;
CC -!- SIMILARITY: Belongs to the 6-phosphogluconate dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; K02072; AAA23918.1; -; Genomic_DNA.
DR EMBL; M63821; AAA24488.1; -; Genomic_DNA.
DR EMBL; M64326; AAA24204.1; -; Genomic_DNA.
DR EMBL; M64327; AAA24205.1; -; Genomic_DNA.
DR EMBL; M64328; AAA24206.1; -; Genomic_DNA.
DR EMBL; M64329; AAA24207.1; -; Genomic_DNA.
DR EMBL; M64330; AAA24208.1; -; Genomic_DNA.
DR EMBL; M64331; AAA24209.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75090.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15869.1; -; Genomic_DNA.
DR EMBL; M23181; AAA23924.1; -; Genomic_DNA.
DR EMBL; M18956; AAA23919.1; -; Genomic_DNA.
DR EMBL; M18957; AAA23920.1; -; Genomic_DNA.
DR EMBL; M18960; AAA23922.1; -; Genomic_DNA.
DR EMBL; AF125322; AAC27540.1; -; Genomic_DNA.
DR PIR; D64968; DEECGC.
DR PIR; I62463; I62463.
DR PIR; I62465; I62465.
DR RefSeq; NP_416533.1; NC_000913.3.
DR RefSeq; WP_000043484.1; NZ_LN832404.1.
DR PDB; 2ZYA; X-ray; 1.60 A; A/B=1-468.
DR PDB; 2ZYD; X-ray; 1.50 A; A/B=1-468.
DR PDB; 3FWN; X-ray; 1.50 A; A/B=1-468.
DR PDBsum; 2ZYA; -.
DR PDBsum; 2ZYD; -.
DR PDBsum; 3FWN; -.
DR AlphaFoldDB; P00350; -.
DR SMR; P00350; -.
DR BioGRID; 4261354; 19.
DR BioGRID; 850901; 1.
DR DIP; DIP-9819N; -.
DR IntAct; P00350; 6.
DR STRING; 511145.b2029; -.
DR jPOST; P00350; -.
DR PaxDb; P00350; -.
DR PRIDE; P00350; -.
DR EnsemblBacteria; AAC75090; AAC75090; b2029.
DR EnsemblBacteria; BAA15869; BAA15869; BAA15869.
DR GeneID; 946554; -.
DR KEGG; ecj:JW2011; -.
DR KEGG; eco:b2029; -.
DR PATRIC; fig|1411691.4.peg.223; -.
DR EchoBASE; EB0406; -.
DR eggNOG; COG0362; Bacteria.
DR HOGENOM; CLU_024540_4_2_6; -.
DR InParanoid; P00350; -.
DR OMA; VIMVKAG; -.
DR PhylomeDB; P00350; -.
DR BioCyc; EcoCyc:6PGLUCONDEHYDROG-MON; -.
DR BioCyc; MetaCyc:6PGLUCONDEHYDROG-MON; -.
DR BRENDA; 1.1.1.44; 2026.
DR SABIO-RK; P00350; -.
DR UniPathway; UPA00115; UER00410.
DR EvolutionaryTrace; P00350; -.
DR PRO; PR:P00350; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0097216; F:guanosine tetraphosphate binding; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0050661; F:NADP binding; IBA:GO_Central.
DR GO; GO:0004616; F:phosphogluconate dehydrogenase (decarboxylating) activity; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IPI:UniProtKB.
DR GO; GO:0046177; P:D-gluconate catabolic process; IMP:EcoCyc.
DR GO; GO:0006098; P:pentose-phosphate shunt; IDA:UniProtKB.
DR GO; GO:0009051; P:pentose-phosphate shunt, oxidative branch; IBA:GO_Central.
DR Gene3D; 1.10.1040.10; -; 1.
DR InterPro; IPR008927; 6-PGluconate_DH-like_C_sf.
DR InterPro; IPR013328; 6PGD_dom2.
DR InterPro; IPR006114; 6PGDH_C.
DR InterPro; IPR006113; 6PGDH_Gnd/GntZ.
DR InterPro; IPR006115; 6PGDH_NADP-bd.
DR InterPro; IPR006184; 6PGdom_BS.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR006183; Pgluconate_DH.
DR PANTHER; PTHR11811; PTHR11811; 1.
DR Pfam; PF00393; 6PGD; 1.
DR Pfam; PF03446; NAD_binding_2; 1.
DR PIRSF; PIRSF000109; 6PGD; 1.
DR PRINTS; PR00076; 6PGDHDRGNASE.
DR SMART; SM01350; 6PGD; 1.
DR SUPFAM; SSF48179; SSF48179; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR00873; gnd; 1.
DR PROSITE; PS00461; 6PGD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Gluconate utilization; NADP; Oxidoreductase; Pentose shunt;
KW Reference proteome.
FT CHAIN 1..468
FT /note="6-phosphogluconate dehydrogenase, decarboxylating"
FT /id="PRO_0000090037"
FT ACT_SITE 183
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|PubMed:19686854"
FT ACT_SITE 190
FT /note="Proton donor"
FT /evidence="ECO:0000269|PubMed:19686854"
FT BINDING 10..15
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 33..35
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 74..76
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 102
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 102
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT BINDING 128..130
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT BINDING 186..187
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 191
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 260
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT BINDING 287
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT BINDING 445
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT BINDING 451
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT VARIANT 2
FT /note="S -> L (in strain: ECOR 70)"
FT VARIANT 32
FT /note="F -> Y (in strain: ECOR 70)"
FT VARIANT 39
FT /note="T -> Q (in strain: O7:K1 / VW187)"
FT VARIANT 52
FT /note="V -> D (in strain: ECOR 10)"
FT VARIANT 55
FT /note="Y -> F (in strain: ECOR 10)"
FT VARIANT 102
FT /note="N -> K (in strain: ECOR 65)"
FT VARIANT 117
FT /note="A -> S (in strain: ECOR 70)"
FT VARIANT 123..125
FT /note="IGT -> YRY (in strain: O7:K1 / VW187)"
FT VARIANT 170
FT /note="V -> F (in strain: ECOR 10)"
FT VARIANT 175
FT /note="A -> S (in strain: ECOR 45)"
FT VARIANT 209
FT /note="N -> S (in strain: ECOR 68)"
FT VARIANT 211
FT /note="T -> S (in strain: ECOR 10 and ECOR 69)"
FT VARIANT 216
FT /note="A -> T (in strain: ECOR 67)"
FT VARIANT 294
FT /note="D -> E (in strain: ECOR 70)"
FT VARIANT 308
FT /note="A -> G (in strain: ECOR 68)"
FT VARIANT 313
FT /note="D -> N (in strain: ECOR 67)"
FT VARIANT 315
FT /note="A -> G (in strain: ECOR 70)"
FT VARIANT 325
FT /note="L -> Q (in strain: ECOR 69)"
FT VARIANT 330
FT /note="I -> S (in strain: ECOR 10)"
FT VARIANT 350
FT /note="D -> A (in strain: ECOR 10 and ECOR 69)"
FT VARIANT 369
FT /note="Q -> R (in strain: ECOR 10)"
FT VARIANT 422
FT /note="S -> A (in strain: ECOR 10, ECOR 65, ECOR 68, ECOR
FT 69 and ECOR 70)"
FT CONFLICT 306
FT /note="P -> R (in Ref. 1; AAA23918)"
FT /evidence="ECO:0000305"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 13..23
FT /evidence="ECO:0007829|PDB:2ZYD"
FT TURN 24..26
FT /evidence="ECO:0007829|PDB:2ZYD"
FT STRAND 29..32
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 36..45
FT /evidence="ECO:0007829|PDB:2ZYD"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 57..62
FT /evidence="ECO:0007829|PDB:2ZYD"
FT STRAND 69..72
FT /evidence="ECO:0007829|PDB:2ZYD"
FT STRAND 76..78
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 79..87
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 88..90
FT /evidence="ECO:0007829|PDB:2ZYD"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 105..117
FT /evidence="ECO:0007829|PDB:2ZYD"
FT STRAND 121..129
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 130..136
FT /evidence="ECO:0007829|PDB:2ZYD"
FT STRAND 139..144
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 146..159
FT /evidence="ECO:0007829|PDB:2ZYD"
FT STRAND 168..170
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 178..208
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 212..224
FT /evidence="ECO:0007829|PDB:2ZYD"
FT TURN 225..227
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 230..240
FT /evidence="ECO:0007829|PDB:2ZYD"
FT STRAND 246..248
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 249..252
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 265..273
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 278..290
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 293..300
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 314..347
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 353..359
FT /evidence="ECO:0007829|PDB:2ZYD"
FT STRAND 361..364
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 370..380
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 387..389
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 391..414
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 419..431
FT /evidence="ECO:0007829|PDB:2ZYD"
FT HELIX 438..449
FT /evidence="ECO:0007829|PDB:2ZYD"
FT STRAND 455..458
FT /evidence="ECO:0007829|PDB:2ZYD"
FT STRAND 460..462
FT /evidence="ECO:0007829|PDB:3FWN"
SQ SEQUENCE 468 AA; 51481 MW; 62A32C84DC596D86 CRC64;
MSKQQIGVVG MAVMGRNLAL NIESRGYTVS IFNRSREKTE EVIAENPGKK LVPYYTVKEF
VESLETPRRI LLMVKAGAGT DAAIDSLKPY LDKGDIIIDG GNTFFQDTIR RNRELSAEGF
NFIGTGVSGG EEGALKGPSI MPGGQKEAYE LVAPILTKIA AVAEDGEPCV TYIGADGAGH
YVKMVHNGIE YGDMQLIAEA YSLLKGGLNL TNEELAQTFT EWNNGELSSY LIDITKDIFT
KKDEDGNYLV DVILDEAANK GTGKWTSQSA LDLGEPLSLI TESVFARYIS SLKDQRVAAS
KVLSGPQAQP AGDKAEFIEK VRRALYLGKI VSYAQGFSQL RAASEEYNWD LNYGEIAKIF
RAGCIIRAQF LQKITDAYAE NPQIANLLLA PYFKQIADDY QQALRDVVAY AVQNGIPVPT
FSAAVAYYDS YRAAVLPANL IQAQRDYFGA HTYKRIDKEG VFHTEWLD
