APSD_PARG4
ID APSD_PARG4 Reviewed; 375 AA.
AC B1G894;
DT 16-JAN-2019, integrated into UniProtKB/Swiss-Prot.
DT 29-APR-2008, sequence version 1.
DT 03-AUG-2022, entry version 39.
DE RecName: Full=D-apiose dehydrogenase {ECO:0000303|PubMed:29867142};
DE EC=1.1.1.420 {ECO:0000269|PubMed:29867142};
GN Name=apsD {ECO:0000303|PubMed:29867142};
GN ORFNames=BgramDRAFT_5562 {ECO:0000312|EMBL:EDT07593.1};
OS Paraburkholderia graminis (strain ATCC 700544 / DSM 17151 / LMG 18924 /
OS NCIMB 13744 / C4D1M).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Paraburkholderia.
OX NCBI_TaxID=396598;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700544 / DSM 17151 / LMG 18924 / NCIMB 13744 / C4D1M;
RG US DOE Joint Genome Institute (JGI-PGF);
RA Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Larimer F., Land M.L., Hauser L.,
RA Tiedje J., Richardson P.;
RT "Sequencing of the draft genome and assembly of Burkholderia graminis
RT C4D1M.";
RL Submitted (MAR-2008) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND PATHWAY.
RX PubMed=29867142; DOI=10.1038/s41589-018-0067-7;
RA Carter M.S., Zhang X., Huang H., Bouvier J.T., Francisco B.S.,
RA Vetting M.W., Al-Obaidi N., Bonanno J.B., Ghosh A., Zallot R.G.,
RA Andersen H.M., Almo S.C., Gerlt J.A.;
RT "Functional assignment of multiple catabolic pathways for D-apiose.";
RL Nat. Chem. Biol. 14:696-705(2018).
CC -!- FUNCTION: Involved in catabolism of D-apiose. Catalyzes oxidation of D-
CC apiose to D-apionolactone. {ECO:0000269|PubMed:29867142}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-apiofuranose + NAD(+) = D-apionolactone + H(+) + NADH;
CC Xref=Rhea:RHEA:57056, ChEBI:CHEBI:15378, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945, ChEBI:CHEBI:141215, ChEBI:CHEBI:141216;
CC EC=1.1.1.420; Evidence={ECO:0000269|PubMed:29867142};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.11 mM for D-apiose {ECO:0000269|PubMed:29867142};
CC Note=kcat is 12 sec(-1). {ECO:0000269|PubMed:29867142};
CC -!- PATHWAY: Carbohydrate metabolism. {ECO:0000269|PubMed:29867142}.
CC -!- SIMILARITY: Belongs to the Gfo/Idh/MocA family. {ECO:0000305}.
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DR EMBL; ABLD01000025; EDT07593.1; -; Genomic_DNA.
DR RefSeq; WP_006052131.1; NZ_ABLD01000025.1.
DR AlphaFoldDB; B1G894; -.
DR SMR; B1G894; -.
DR EnsemblBacteria; EDT07593; EDT07593; BgramDRAFT_5562.
DR Proteomes; UP000005045; Unassembled WGS sequence.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR GO; GO:0005975; P:carbohydrate metabolic process; IEA:UniProtKB-KW.
DR InterPro; IPR004104; Gfo/Idh/MocA-like_OxRdtase_C.
DR InterPro; IPR000683; Gfo/Idh/MocA-like_OxRdtase_N.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF01408; GFO_IDH_MocA; 1.
DR Pfam; PF02894; GFO_IDH_MocA_C; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
PE 1: Evidence at protein level;
KW Carbohydrate metabolism; Magnesium; Metal-binding; NAD; Nucleotide-binding;
KW Oxidoreductase.
FT CHAIN 1..375
FT /note="D-apiose dehydrogenase"
FT /id="PRO_0000446034"
FT BINDING 29..30
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
FT BINDING 38
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
FT BINDING 39
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
FT BINDING 41
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
FT BINDING 44
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
FT BINDING 51
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
FT BINDING 93
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
FT BINDING 111..112
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
FT BINDING 112
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
FT BINDING 140
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
FT BINDING 179..181
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
FT BINDING 179
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
FT BINDING 192
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
FT BINDING 196
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
FT BINDING 246
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:B9JK80"
SQ SEQUENCE 375 AA; 40406 MW; 4A39F2AB1C000F32 CRC64;
MSATDATQVI SATTTTVKRF KGALIGCGFF SRNHLHAWRD IDGAEIVALC DADSERLRAA
GQAFGIERLY RDAAAMLSAE QLDFVDIATT APSHRSLVEL AAQAGVAAIC QKPFALTLAD
ARAMVAACER AGVPLMVHEN FRWQPAIQAV GRALRDGAIG TPFWGRVSFR SAFDVFSGQP
YLARNERFIV EDLGIHILDI ARFLFGDVTR LAAATSRVNS AIAGEDVATI LLTHESGVTS
VVDCSYASRQ ARELFPQTLV EVDGAEGTLR LSADYRLEIH NRDGTRTATA APPPLAWASV
PWEAIQASVV NIQRHWIACL RNGGEPQTSG RDNLKTLALV EATYLSAREG RTVELKSLEA
EAPAVTSTSS GAVRR
