6PGD_LACLM
ID 6PGD_LACLM Reviewed; 472 AA.
AC P96789; A2RIU0;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2007, sequence version 3.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=6-phosphogluconate dehydrogenase, decarboxylating;
DE EC=1.1.1.44;
GN Name=gnd; OrderedLocusNames=llmg_0586;
OS Lactococcus lactis subsp. cremoris (strain MG1363).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Lactococcus; Lactococcus cremoris subsp. cremoris.
OX NCBI_TaxID=416870;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9931298; DOI=10.1042/bj3380055;
RA Tetaud E., Hanau S., Wells J.M., Le Page R.W.F., Adams M.J., Arkison S.,
RA Barrett M.P.;
RT "6-phosphogluconate dehydrogenase from Lactococcus lactis: a role for
RT arginine residues in binding substrate and coenzyme.";
RL Biochem. J. 338:55-60(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MG1363;
RX PubMed=17307855; DOI=10.1128/jb.01768-06;
RA Wegmann U., O'Connell-Motherway M., Zomer A., Buist G., Shearman C.,
RA Canchaya C., Ventura M., Goesmann A., Gasson M.J., Kuipers O.P.,
RA van Sinderen D., Kok J.;
RT "The complete genome sequence of the lactic acid bacterial paradigm
RT Lactococcus lactis subsp. cremoris MG1363.";
RL J. Bacteriol. 189:3256-3270(2007).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE; PRODUCT;
RP INHIBITORS AND NADP, SUBUNIT, AND ACTIVE SITE.
RX PubMed=17222187; DOI=10.1111/j.1742-4658.2006.05585.x;
RA Sundaramoorthy R., Iulek J., Barrett M.P., Bidet O., Ruda G.F.,
RA Gilbert I.H., Hunter W.N.;
RT "Crystal structures of a bacterial 6-phosphogluconate dehydrogenase reveal
RT aspects of specificity, mechanism and mode of inhibition by analogues of
RT high-energy reaction intermediates.";
RL FEBS J. 274:275-286(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:0000250}.
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 -!- 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:0000250}.
CC -!- SIMILARITY: Belongs to the 6-phosphogluconate dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; U74322; AAC12804.1; -; Genomic_DNA.
DR EMBL; AM406671; CAL97186.1; -; Genomic_DNA.
DR RefSeq; WP_011834606.1; NZ_WJVF01000015.1.
DR PDB; 2IYO; X-ray; 2.40 A; A=1-472.
DR PDB; 2IYP; X-ray; 2.79 A; A/B/C=1-472.
DR PDB; 2IZ0; X-ray; 2.60 A; A/B/C=1-472.
DR PDB; 2IZ1; X-ray; 2.30 A; A/B/C=1-472.
DR PDBsum; 2IYO; -.
DR PDBsum; 2IYP; -.
DR PDBsum; 2IZ0; -.
DR PDBsum; 2IZ1; -.
DR AlphaFoldDB; P96789; -.
DR SMR; P96789; -.
DR STRING; 416870.llmg_0586; -.
DR EnsemblBacteria; CAL97186; CAL97186; llmg_0586.
DR KEGG; llm:llmg_0586; -.
DR eggNOG; COG0362; Bacteria.
DR HOGENOM; CLU_024540_4_2_9; -.
DR OMA; VIMVKAG; -.
DR PhylomeDB; P96789; -.
DR BioCyc; LLAC416870:LLMG_RS03045-MON; -.
DR BRENDA; 1.1.1.44; 2903.
DR SABIO-RK; P96789; -.
DR UniPathway; UPA00115; UER00410.
DR EvolutionaryTrace; P96789; -.
DR Proteomes; UP000000364; Chromosome.
DR GO; GO:0050661; F:NADP binding; IEA:InterPro.
DR GO; GO:0004616; F:phosphogluconate dehydrogenase (decarboxylating) activity; IEA:UniProtKB-EC.
DR GO; GO:0019521; P:D-gluconate metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0016054; P:organic acid catabolic process; IEA:UniProt.
DR GO; GO:0006098; P:pentose-phosphate shunt; IEA:UniProtKB-UniPathway.
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.
FT CHAIN 1..472
FT /note="6-phosphogluconate dehydrogenase, decarboxylating"
FT /id="PRO_0000090046"
FT ACT_SITE 184
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|PubMed:17222187"
FT ACT_SITE 191
FT /note="Proton donor"
FT /evidence="ECO:0000269|PubMed:17222187"
FT BINDING 10..15
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:17222187"
FT BINDING 33..35
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:17222187"
FT BINDING 74..76
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:17222187"
FT BINDING 102
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:17222187"
FT BINDING 102
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:17222187"
FT BINDING 128..130
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:17222187"
FT BINDING 187..188
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:17222187"
FT BINDING 192
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:17222187"
FT BINDING 262
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:17222187"
FT BINDING 289
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000269|PubMed:17222187"
FT BINDING 447
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000269|PubMed:17222187"
FT BINDING 453
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000269|PubMed:17222187"
FT CONFLICT 43
FT /note="Y -> F (in Ref. 1; AAC12804)"
FT /evidence="ECO:0000305"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 13..24
FT /evidence="ECO:0007829|PDB:2IZ1"
FT STRAND 29..32
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 36..45
FT /evidence="ECO:0007829|PDB:2IZ1"
FT TURN 46..48
FT /evidence="ECO:0007829|PDB:2IZ1"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 57..62
FT /evidence="ECO:0007829|PDB:2IZ1"
FT STRAND 69..72
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 78..87
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 88..90
FT /evidence="ECO:0007829|PDB:2IZ1"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 105..114
FT /evidence="ECO:0007829|PDB:2IZ1"
FT TURN 115..117
FT /evidence="ECO:0007829|PDB:2IZ1"
FT STRAND 121..127
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 130..136
FT /evidence="ECO:0007829|PDB:2IZ1"
FT STRAND 140..144
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 146..159
FT /evidence="ECO:0007829|PDB:2IZ1"
FT TURN 164..166
FT /evidence="ECO:0007829|PDB:2IZ1"
FT STRAND 169..171
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 179..207
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 213..223
FT /evidence="ECO:0007829|PDB:2IZ1"
FT TURN 224..228
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 231..239
FT /evidence="ECO:0007829|PDB:2IZ1"
FT STRAND 245..250
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 251..254
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 264..275
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 280..293
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 295..304
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 316..349
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 355..361
FT /evidence="ECO:0007829|PDB:2IZ1"
FT STRAND 363..365
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 373..382
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 389..391
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 393..416
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 421..433
FT /evidence="ECO:0007829|PDB:2IZ1"
FT HELIX 440..451
FT /evidence="ECO:0007829|PDB:2IZ1"
FT STRAND 457..462
FT /evidence="ECO:0007829|PDB:2IZ1"
SQ SEQUENCE 472 AA; 52460 MW; A0075C9F46171F1C CRC64;
MAQANFGVVG MAVMGKNLAL NVESRGYTVA IYNRTTSKTE EVYKEHQDKN LVFTKTLEEF
VGSLEKPRRI MLMVQAGAAT DATIKSLLPL LDIGDILIDG GNTHFPDTMR RNAELADSGI
NFIGTGVSGG EKGALLGPSM MPGGQKEAYD LVAPIFEQIA AKAPQDGKPC VAYMGANGAG
HYVKMVHNGI EYGDMQLIAE SYDLLKRILG LSNAEIQAIF EEWNEGELDS YLIEITKEVL
KRKDDEGEGY IVDKILDKAG NKGTGKWTSE SALDLGVPLP LITESVFARY ISTYKDERVK
ASKVLSGPAL DFSGDKKEVI EKIRKALYFS KIMSYAQGFA QLRKASEEFD WDLPYGTIAQ
IWRAGCIIRA EFLQNITDAF DKDSELENLL LDDYFVDITK RYQEAVRDVV SLAVQAGTPI
PTFTSAISYY DSYRSENLPA NLIQAQRDYF GAHTYERTDK AGIFHYDWYT ED
