GLCDH_HALMT
ID GLCDH_HALMT Reviewed; 357 AA.
AC Q977U7; I3R3J6;
DT 25-JAN-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=Glucose 1-dehydrogenase {ECO:0000255|HAMAP-Rule:MF_02127};
DE Short=GDH {ECO:0000255|HAMAP-Rule:MF_02127};
DE Short=GlcDH {ECO:0000255|HAMAP-Rule:MF_02127};
DE EC=1.1.1.47 {ECO:0000255|HAMAP-Rule:MF_02127, ECO:0000269|PubMed:11425479, ECO:0000269|PubMed:8925901};
GN Name=gdh {ECO:0000312|EMBL:AFK18806.1}; OrderedLocusNames=HFX_1090;
OS Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC
OS 14739 / NCIMB 2177 / R-4) (Halobacterium mediterranei).
OC Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Haloferacales;
OC Haloferacaceae; Haloferax.
OX NCBI_TaxID=523841;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, AND
RP SUBUNIT.
RC STRAIN=ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4;
RX PubMed=11425479; DOI=10.1111/j.1574-6968.2001.tb10719.x;
RA Pire C., Esclapez J., Ferrer J., Bonete M.J.;
RT "Heterologous overexpression of glucose dehydrogenase from the halophilic
RT archaeon Haloferax mediterranei, an enzyme of the medium chain
RT dehydrogenase/reductase family.";
RL FEMS Microbiol. Lett. 200:221-227(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4;
RX PubMed=22843593; DOI=10.1128/jb.00880-12;
RA Han J., Zhang F., Hou J., Liu X., Li M., Liu H., Cai L., Zhang B., Chen Y.,
RA Zhou J., Hu S., Xiang H.;
RT "Complete genome sequence of the metabolically versatile halophilic
RT archaeon Haloferax mediterranei, a poly(3-hydroxybutyrate-co-3-
RT hydroxyvalerate) producer.";
RL J. Bacteriol. 194:4463-4464(2012).
RN [3]
RP PROTEIN SEQUENCE OF 1-17, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE
RP SPECIFICITY, KINETIC PARAMETERS, ACTIVITY REGULATION, INDUCTION, AND
RP SUBUNIT.
RC STRAIN=ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4;
RX PubMed=8925901; DOI=10.1016/0014-5793(96)00235-9;
RA Bonete M.J., Pire C., Llorca F.I., Camacho M.L.;
RT "Glucose dehydrogenase from the halophilic Archaeon Haloferax mediterranei:
RT enzyme purification, characterisation and N-terminal sequence.";
RL FEBS Lett. 383:227-229(1996).
RN [4]
RP PROTEIN SEQUENCE OF 1-38, COFACTOR, KINETIC PARAMETERS, ACTIVITY
RP REGULATION, MASS SPECTROMETRY, AND KINETIC MECHANISM.
RC STRAIN=ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4;
RX DOI=10.1016/S1381-1177(99)00113-7;
RA Pire C., Camacho M.L., Ferrer J., Hough D.W., Bonete M.J.;
RT "NAD(P)(+)-glucose dehydrogenase from Haloferax mediterranei: kinetic
RT mechanism and metal content.";
RL J. Mol. Catal., B Enzym. 10:409-417(2000).
RN [5]
RP CRYSTALLIZATION.
RC STRAIN=ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4;
RX PubMed=11717506; DOI=10.1107/s0907444901015189;
RA Ferrer J., Fisher M., Burke J., Sedelnikova S.E., Baker P.J., Gilmour D.J.,
RA Bonete M.J., Pire C., Esclapez J., Rice D.W.;
RT "Crystallization and preliminary X-ray analysis of glucose dehydrogenase
RT from Haloferax mediterranei.";
RL Acta Crystallogr. D 57:1887-1889(2001).
RN [6]
RP CRYSTALLIZATION.
RC STRAIN=ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4;
RX PubMed=16511145; DOI=10.1107/s1744309105019949;
RA Esclapez J., Britton K.L., Baker P.J., Fisher M., Pire C., Ferrer J.,
RA Bonete M.J., Rice D.W.;
RT "Crystallization and preliminary X-ray analysis of binary and ternary
RT complexes of Haloferax mediterranei glucose dehydrogenase.";
RL Acta Crystallogr. F 61:743-746(2005).
RN [7]
RP MUTAGENESIS OF ASP-172; ASP-216 AND ASP-344.
RC STRAIN=ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4;
RX PubMed=17289028; DOI=10.1016/j.febslet.2007.01.054;
RA Esclapez J., Pire C., Bautista V., Martinez-Espinosa R.M., Ferrer J.,
RA Bonete M.J.;
RT "Analysis of acidic surface of Haloferax mediterranei glucose dehydrogenase
RT by site-directed mutagenesis.";
RL FEBS Lett. 581:837-842(2007).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF WILD-TYPE AND MUTANT CYS-38 IN
RP COMPLEX WITH NADP AND ZINC.
RC STRAIN=ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4;
RX PubMed=16551747; DOI=10.1073/pnas.0508854103;
RA Britton K.L., Baker P.J., Fisher M., Ruzheinikov S., Gilmour D.J.,
RA Bonete M.J., Ferrer J., Pire C., Esclapez J., Rice D.W.;
RT "Analysis of protein solvent interactions in glucose dehydrogenase from the
RT extreme halophile Haloferax mediterranei.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:4846-4851(2006).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEXES WITH BETA-D-GLUCOSE;
RP D-GLUCONO-1,5-LACTONE; NADP AND ZINC, AND REACTION MECHANISM.
RC STRAIN=ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4;
RX PubMed=19131516; DOI=10.1073/pnas.0807529106;
RA Baker P.J., Britton K.L., Fisher M., Esclapez J., Pire C., Bonete M.J.,
RA Ferrer J., Rice D.W.;
RT "Active site dynamics in the zinc-dependent medium chain alcohol
RT dehydrogenase superfamily.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:779-784(2009).
CC -!- FUNCTION: Catalyzes the NAD(P)(+)-dependent oxidation of D-glucose to
CC D-gluconate. Displays broad substrate specificity since it is able to
CC catalyze the oxidation of a number of alternative aldose sugars, such
CC as D-xylose, D-galactose, and D-fucose, to the corresponding glyconate.
CC Can utilize both NAD(+) and NADP(+) as electron acceptor, with a
CC preference for NADP(+). Physiologically, seems to be involved in the
CC degradation of glucose through a modified Entner-Doudoroff pathway.
CC {ECO:0000269|PubMed:11425479, ECO:0000269|PubMed:8925901}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-glucose + NAD(+) = D-glucono-1,5-lactone + H(+) + NADH;
CC Xref=Rhea:RHEA:14293, ChEBI:CHEBI:4167, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16217, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.1.1.47;
CC Evidence={ECO:0000269|PubMed:11425479, ECO:0000269|PubMed:8925901};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-glucose + NADP(+) = D-glucono-1,5-lactone + H(+) + NADPH;
CC Xref=Rhea:RHEA:14405, ChEBI:CHEBI:4167, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16217, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349; EC=1.1.1.47;
CC Evidence={ECO:0000269|PubMed:11425479, ECO:0000269|PubMed:8925901};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000269|Ref.4};
CC Note=Binds 2 Zn(2+) ions per subunit. One of the zinc atoms is
CC essential for catalytic activity while the other has a structural
CC function, according to Ref.4. However, the crystal structures show a
CC single zinc ion, the catalytic one. {ECO:0000269|Ref.4};
CC -!- ACTIVITY REGULATION: Activated by molar concentrations of KCl or NaCl.
CC Inhibited by EDTA in vitro. {ECO:0000269|PubMed:8925901,
CC ECO:0000269|Ref.4}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.2 mM for NAD(+) (at 40 degrees Celsius and pH 8.8)
CC {ECO:0000269|PubMed:8925901};
CC KM=0.024 mM for NADP(+) (at 40 degrees Celsius and pH 8.8)
CC {ECO:0000269|PubMed:8925901};
CC KM=3.9 mM for beta-D-glucose (in the presence of NADP(+), at 40
CC degrees Celsius and pH 8.8) {ECO:0000269|PubMed:8925901};
CC KM=4.7 mM for D-glucose (at 40 degrees Celsius and pH 8.8)
CC {ECO:0000269|Ref.4};
CC KM=6.9 mM for D-xylose (at 40 degrees Celsius and pH 8.8)
CC {ECO:0000269|Ref.4};
CC Vmax=93 umol/min/mg enzyme for the oxidation of D-glucose by NADP(+)
CC (at 40 degrees Celsius and pH 8.8) {ECO:0000269|Ref.4};
CC Vmax=80 umol/min/mg enzyme for the oxidation of D-xylose by NADP(+)
CC (at 40 degrees Celsius and pH 8.8) {ECO:0000269|Ref.4};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:11425479,
CC ECO:0000269|PubMed:16551747, ECO:0000269|PubMed:8925901}.
CC -!- INTERACTION:
CC Q977U7; Q977U7: gdh; NbExp=2; IntAct=EBI-15576464, EBI-15576464;
CC -!- INDUCTION: Up-regulated by glucose. {ECO:0000269|PubMed:8925901}.
CC -!- MASS SPECTROMETRY: Mass=39248; Mass_error=4; Method=Electrospray;
CC Evidence={ECO:0000269|Ref.4};
CC -!- MISCELLANEOUS: The reaction follows an ordered Bi-Bi kinetic mechanism,
CC involving an ordered binding of NADP(+) and D-glucose, followed by an
CC ordered released of gluconolactone and NADPH.
CC {ECO:0000269|PubMed:19131516}.
CC -!- SIMILARITY: Belongs to the zinc-containing alcohol dehydrogenase
CC family. Glucose 1-dehydrogenase subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_02127}.
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DR EMBL; AJ251111; CAC42505.1; -; Genomic_DNA.
DR EMBL; CP001868; AFK18806.1; -; Genomic_DNA.
DR PIR; S66213; S66213.
DR RefSeq; WP_004572583.1; NZ_CP039139.1.
DR PDB; 2B5V; X-ray; 2.00 A; A=1-357.
DR PDB; 2B5W; X-ray; 1.60 A; A=1-357.
DR PDB; 2VWG; X-ray; 2.00 A; A=1-357.
DR PDB; 2VWH; X-ray; 2.03 A; A=1-357.
DR PDB; 2VWP; X-ray; 2.01 A; A=1-357.
DR PDB; 2VWQ; X-ray; 2.10 A; A=1-357.
DR PDBsum; 2B5V; -.
DR PDBsum; 2B5W; -.
DR PDBsum; 2VWG; -.
DR PDBsum; 2VWH; -.
DR PDBsum; 2VWP; -.
DR PDBsum; 2VWQ; -.
DR AlphaFoldDB; Q977U7; -.
DR SMR; Q977U7; -.
DR DIP; DIP-48672N; -.
DR STRING; 523841.HFX_1090; -.
DR EnsemblBacteria; AFK18806; AFK18806; HFX_1090.
DR GeneID; 40156447; -.
DR KEGG; hme:HFX_1090; -.
DR eggNOG; arCOG01459; Archaea.
DR HOGENOM; CLU_026673_1_0_2; -.
DR OMA; MCRNGRY; -.
DR OrthoDB; 43162at2157; -.
DR BioCyc; MetaCyc:MON-4902; -.
DR BRENDA; 1.1.1.113; 2566.
DR BRENDA; 1.1.1.119; 2566.
DR BRENDA; 1.1.1.175; 2566.
DR BRENDA; 1.1.1.47; 2566.
DR EvolutionaryTrace; Q977U7; -.
DR Proteomes; UP000006469; Chromosome.
DR GO; GO:0047934; F:glucose 1-dehydrogenase (NAD+) activity; IEA:RHEA.
DR GO; GO:0047935; F:glucose 1-dehydrogenase (NADP+) activity; IEA:RHEA.
DR GO; GO:0047936; F:glucose 1-dehydrogenase [NAD(P)] activity; IDA:UniProtKB.
DR GO; GO:0005536; F:glucose binding; IDA:UniProtKB.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0070403; F:NAD+ binding; IDA:UniProtKB.
DR GO; GO:0070401; F:NADP+ binding; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; IDA:UniProtKB.
DR GO; GO:0019595; P:non-phosphorylated glucose catabolic process; IDA:UniProtKB.
DR HAMAP; MF_02127; Glucose_DH; 1.
DR InterPro; IPR013154; ADH_N.
DR InterPro; IPR026583; Glc_1-DH_arc.
DR InterPro; IPR031640; Glu_dehyd_C.
DR InterPro; IPR011032; GroES-like_sf.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF08240; ADH_N; 1.
DR Pfam; PF16912; Glu_dehyd_C; 1.
DR SUPFAM; SSF50129; SSF50129; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Direct protein sequencing;
KW Metal-binding; NAD; NADP; Nucleotide-binding; Oxidoreductase; Zinc.
FT CHAIN 1..357
FT /note="Glucose 1-dehydrogenase"
FT /id="PRO_0000414832"
FT BINDING 38
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:16551747,
FT ECO:0000269|PubMed:19131516"
FT BINDING 40
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:19131516"
FT BINDING 49
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:19131516"
FT BINDING 63
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:16551747,
FT ECO:0000269|PubMed:19131516"
FT BINDING 64
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:16551747,
FT ECO:0000269|PubMed:19131516"
FT BINDING 114
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:19131516"
FT BINDING 150
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:19131516"
FT BINDING 150
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:16551747,
FT ECO:0000269|PubMed:19131516"
FT BINDING 181..184
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:16551747,
FT ECO:0000269|PubMed:19131516"
FT BINDING 207..208
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:16551747,
FT ECO:0000269|PubMed:19131516"
FT BINDING 228
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:16551747,
FT ECO:0000269|PubMed:19131516"
FT BINDING 272..274
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:16551747,
FT ECO:0000269|PubMed:19131516"
FT BINDING 301..303
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:16551747,
FT ECO:0000269|PubMed:19131516"
FT BINDING 303
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:19131516"
FT MUTAGEN 172
FT /note="D->K: Does not affect the kinetic parameters but
FT results in a slightly less halotolerant protein."
FT /evidence="ECO:0000269|PubMed:17289028"
FT MUTAGEN 216
FT /note="D->K: Does not affect the kinetic parameters but
FT results in a slightly less halotolerant protein."
FT /evidence="ECO:0000269|PubMed:17289028"
FT MUTAGEN 344
FT /note="D->K: Does not affect the kinetic parameters and has
FT no effect on the salt activity profile."
FT /evidence="ECO:0000269|PubMed:17289028"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 14..17
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 27..37
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 39..46
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 47..49
FT /evidence="ECO:0007829|PDB:2VWQ"
FT STRAND 57..60
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 63..71
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 82..85
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 87..89
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 97..100
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 104..106
FT /evidence="ECO:0007829|PDB:2B5W"
FT TURN 115..117
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 118..120
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 125..131
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 132..134
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 135..137
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 140..142
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 146..148
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 149..164
FT /evidence="ECO:0007829|PDB:2B5W"
FT TURN 165..168
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 175..179
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 183..194
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 201..206
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 213..220
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 224..227
FT /evidence="ECO:0007829|PDB:2B5W"
FT TURN 228..230
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 233..235
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 236..239
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 243..248
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 253..262
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 263..271
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 284..293
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 297..300
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 306..318
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 321..327
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 328..333
FT /evidence="ECO:0007829|PDB:2B5W"
FT HELIX 334..341
FT /evidence="ECO:0007829|PDB:2B5W"
FT STRAND 349..353
FT /evidence="ECO:0007829|PDB:2B5W"
SQ SEQUENCE 357 AA; 39242 MW; E19ABC275A31BCBA CRC64;
MKAIAVKRGE DRPVVIEKPR PEPESGEALV RTLRVGVDGT DHEVIAGGHG GFPEGEDHLV
LGHEAVGVVV DPNDTELEEG DIVVPTVRRP PASGTNEYFE RDQPDMAPDG MYFERGIVGA
HGYMSEFFTS PEKYLVRIPR SQAELGFLIE PISITEKALE HAYASRSAFD WDPSSAFVLG
NGSLGLLTLA MLKVDDKGYE NLYCLGRRDR PDPTIDIIEE LDATYVDSRQ TPVEDVPDVY
EQMDFIYEAT GFPKHAIQSV QALAPNGVGA LLGVPSDWAF EVDAGAFHRE MVLHNKALVG
SVNSHVEHFE AATVTFTKLP KWFLEDLVTG VHPLSEFEAA FDDDDTTIKT AIEFSTV
