6PGD1_YEAST
ID 6PGD1_YEAST Reviewed; 489 AA.
AC P38720; D3DLD1;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 197.
DE RecName: Full=6-phosphogluconate dehydrogenase, decarboxylating 1;
DE EC=1.1.1.44;
GN Name=GND1; OrderedLocusNames=YHR183W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Desouza M., Lobo Z., Maitra P.K.;
RL Submitted (NOV-1994) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8091229; DOI=10.1126/science.8091229;
RA Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z.,
RA Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T.,
RA Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P., Louis E.J.,
RA Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L.,
RA St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P.,
RA Waterston R., Wilson R., Vaudin M.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
RT VIII.";
RL Science 265:2077-2082(1994).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP PROTEIN SEQUENCE OF 41-47 AND 120-131.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7895733; DOI=10.1002/elps.11501501210;
RA Garrels J.I., Futcher B., Kobayashi R., Latter G.I., Schwender B.,
RA Volpe T., Warner J.R., McLaughlin C.S.;
RT "Protein identifications for a Saccharomyces cerevisiae protein database.";
RL Electrophoresis 15:1466-1486(1994).
RN [5]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [6]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-50, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.37 ANGSTROMS) IN COMPLEX WITH CITRATE, CATALYTIC
RP ACTIVITY, FUNCTION, SUBUNIT, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=17570834; DOI=10.1186/1472-6807-7-38;
RA He W., Wang Y., Liu W., Zhou C.Z.;
RT "Crystal structure of Saccharomyces cerevisiae 6-phosphogluconate
RT dehydrogenase Gnd1.";
RL BMC Struct. Biol. 7:38-38(2007).
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:17570834}.
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:17570834};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=50 uM for 6-phosphogluconate {ECO:0000269|PubMed:17570834};
CC KM=35 uM for NADP {ECO:0000269|PubMed:17570834};
CC -!- PATHWAY: Carbohydrate degradation; pentose phosphate pathway; D-
CC ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage): step
CC 3/3.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:17570834}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 101000 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the 6-phosphogluconate dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; Z46631; CAA86600.1; -; Genomic_DNA.
DR EMBL; U00028; AAB68452.1; -; Genomic_DNA.
DR EMBL; U17155; AAA53637.1; -; Genomic_DNA.
DR EMBL; BK006934; DAA06875.1; -; Genomic_DNA.
DR PIR; S46671; S46671.
DR RefSeq; NP_012053.3; NM_001179314.3.
DR PDB; 2P4Q; X-ray; 2.37 A; A=1-489.
DR PDBsum; 2P4Q; -.
DR AlphaFoldDB; P38720; -.
DR SMR; P38720; -.
DR BioGRID; 36616; 169.
DR DIP; DIP-6604N; -.
DR IntAct; P38720; 137.
DR MINT; P38720; -.
DR STRING; 4932.YHR183W; -.
DR iPTMnet; P38720; -.
DR MaxQB; P38720; -.
DR PaxDb; P38720; -.
DR PRIDE; P38720; -.
DR TopDownProteomics; P38720; -.
DR EnsemblFungi; YHR183W_mRNA; YHR183W; YHR183W.
DR GeneID; 856589; -.
DR KEGG; sce:YHR183W; -.
DR SGD; S000001226; GND1.
DR VEuPathDB; FungiDB:YHR183W; -.
DR eggNOG; KOG2653; Eukaryota.
DR GeneTree; ENSGT00390000009023; -.
DR HOGENOM; CLU_024540_4_2_1; -.
DR InParanoid; P38720; -.
DR OMA; VIMVKAG; -.
DR BioCyc; YEAST:YHR183W-MON; -.
DR BRENDA; 1.1.1.44; 984.
DR Reactome; R-SCE-71336; Pentose phosphate pathway.
DR SABIO-RK; P38720; -.
DR UniPathway; UPA00115; UER00410.
DR EvolutionaryTrace; P38720; -.
DR PRO; PR:P38720; -.
DR Proteomes; UP000002311; Chromosome VIII.
DR RNAct; P38720; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR GO; GO:0050661; F:NADP binding; IBA:GO_Central.
DR GO; GO:0004616; F:phosphogluconate dehydrogenase (decarboxylating) activity; IMP:SGD.
DR GO; GO:0034599; P:cellular response to oxidative stress; IMP:SGD.
DR GO; GO:0046177; P:D-gluconate catabolic process; IBA:GO_Central.
DR GO; GO:0009051; P:pentose-phosphate shunt, oxidative branch; IMP:SGD.
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; Cytoplasm; Direct protein sequencing; Gluconate utilization;
KW NADP; Oxidoreductase; Pentose shunt; Phosphoprotein; Reference proteome.
FT CHAIN 1..489
FT /note="6-phosphogluconate dehydrogenase, decarboxylating 1"
FT /id="PRO_0000090075"
FT ACT_SITE 182
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 189
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 9..14
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 32..34
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 74..76
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
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 /evidence="ECO:0000250"
FT BINDING 128..130
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 185..186
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 190
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 259
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 286
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 446
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250"
FT BINDING 452
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250"
FT MOD_RES 50
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT STRAND 4..8
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 12..23
FT /evidence="ECO:0007829|PDB:2P4Q"
FT STRAND 28..31
FT /evidence="ECO:0007829|PDB:2P4Q"
FT STRAND 33..35
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 36..43
FT /evidence="ECO:0007829|PDB:2P4Q"
FT TURN 44..48
FT /evidence="ECO:0007829|PDB:2P4Q"
FT STRAND 49..52
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 57..62
FT /evidence="ECO:0007829|PDB:2P4Q"
FT STRAND 69..72
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 78..87
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 88..90
FT /evidence="ECO:0007829|PDB:2P4Q"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 105..117
FT /evidence="ECO:0007829|PDB:2P4Q"
FT STRAND 121..129
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 130..136
FT /evidence="ECO:0007829|PDB:2P4Q"
FT STRAND 139..144
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 146..148
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 149..159
FT /evidence="ECO:0007829|PDB:2P4Q"
FT STRAND 166..168
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 177..205
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 211..222
FT /evidence="ECO:0007829|PDB:2P4Q"
FT TURN 223..226
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 229..238
FT /evidence="ECO:0007829|PDB:2P4Q"
FT STRAND 245..247
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 248..251
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 261..272
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 277..290
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 292..301
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 315..348
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 354..362
FT /evidence="ECO:0007829|PDB:2P4Q"
FT STRAND 363..365
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 370..381
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 388..390
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 392..415
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 420..432
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 439..449
FT /evidence="ECO:0007829|PDB:2P4Q"
FT HELIX 458..460
FT /evidence="ECO:0007829|PDB:2P4Q"
FT STRAND 463..465
FT /evidence="ECO:0007829|PDB:2P4Q"
SQ SEQUENCE 489 AA; 53543 MW; 55CAE5DACDC6A00B CRC64;
MSADFGLIGL AVMGQNLILN AADHGFTVCA YNRTQSKVDH FLANEAKGKS IIGATSIEDF
ISKLKRPRKV MLLVKAGAPV DALINQIVPL LEKGDIIIDG GNSHFPDSNR RYEELKKKGI
LFVGSGVSGG EEGARYGPSL MPGGSEEAWP HIKNIFQSIS AKSDGEPCCE WVGPAGAGHY
VKMVHNGIEY GDMQLICEAY DIMKRLGGFT DKEISDVFAK WNNGVLDSFL VEITRDILKF
DDVDGKPLVE KIMDTAGQKG TGKWTAINAL DLGMPVTLIG EAVFARCLSA LKNERIRASK
VLPGPEVPKD AVKDREQFVD DLEQALYASK IISYAQGFML IREAAATYGW KLNNPAIALM
WRGGCIIRSV FLGQITKAYR EEPDLENLLF NKFFADAVTK AQSGWRKSIA LATTYGIPTP
AFSTALSFYD GYRSERLPAN LLQAQRDYFG AHTFRVLPEC ASDNLPVDKD IHINWTGHGG
NVSSSTYQA
