APSD_AGRRK
ID APSD_AGRRK Reviewed; 345 AA.
AC B9JK80;
DT 16-JAN-2019, integrated into UniProtKB/Swiss-Prot.
DT 24-MAR-2009, sequence version 1.
DT 03-AUG-2022, entry version 70.
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 OrderedLocusNames=Arad_9238 {ECO:0000312|EMBL:ACM30322.1};
OS Agrobacterium radiobacter (strain K84 / ATCC BAA-868).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium;
OC Agrobacterium tumefaciens complex.
OX NCBI_TaxID=311403;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K84 / ATCC BAA-868;
RX PubMed=19251847; DOI=10.1128/jb.01779-08;
RA Slater S.C., Goldman B.S., Goodner B., Setubal J.C., Farrand S.K.,
RA Nester E.W., Burr T.J., Banta L., Dickerman A.W., Paulsen I., Otten L.,
RA Suen G., Welch R., Almeida N.F., Arnold F., Burton O.T., Du Z., Ewing A.,
RA Godsy E., Heisel S., Houmiel K.L., Jhaveri J., Lu J., Miller N.M.,
RA Norton S., Chen Q., Phoolcharoen W., Ohlin V., Ondrusek D., Pride N.,
RA Stricklin S.L., Sun J., Wheeler C., Wilson L., Zhu H., Wood D.W.;
RT "Genome sequences of three Agrobacterium biovars help elucidate the
RT evolution of multichromosome genomes in bacteria.";
RL J. Bacteriol. 191:2501-2511(2009).
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).
RN [3] {ECO:0007744|PDB:5UHW, ECO:0007744|PDB:5UHZ, ECO:0007744|PDB:5UI9, ECO:0007744|PDB:5UIA, ECO:0007744|PDB:5UIB}
RP X-RAY CRYSTALLOGRAPHY (1.92 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM; NAD AND
RP SUBSTRATE ANALOGS.
RA Cook W.J., Bonanno J.B., Fedorov E., Huang H., Gerlt J.A., Almo S.C.;
RL Submitted (JAN-2017) to the PDB data bank.
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=0.078 mM for D-apiose {ECO:0000269|PubMed:29867142};
CC Note=kcat is 53 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; CP000629; ACM30322.1; -; Genomic_DNA.
DR PDB; 5UHW; X-ray; 2.24 A; A/B=1-345.
DR PDB; 5UHZ; X-ray; 2.20 A; A/B=1-345.
DR PDB; 5UI9; X-ray; 1.92 A; A/B=1-345.
DR PDB; 5UIA; X-ray; 2.18 A; A/B=1-345.
DR PDB; 5UIB; X-ray; 2.65 A; A/B=1-345.
DR PDBsum; 5UHW; -.
DR PDBsum; 5UHZ; -.
DR PDBsum; 5UI9; -.
DR PDBsum; 5UIA; -.
DR PDBsum; 5UIB; -.
DR AlphaFoldDB; B9JK80; -.
DR SMR; B9JK80; -.
DR STRING; 311403.Arad_9238; -.
DR EnsemblBacteria; ACM30322; ACM30322; Arad_9238.
DR KEGG; ara:Arad_9238; -.
DR eggNOG; COG0673; Bacteria.
DR HOGENOM; CLU_023194_1_4_5; -.
DR OMA; LMVHENF; -.
DR BioCyc; MetaCyc:MON-20958; -.
DR BRENDA; 1.1.1.420; 200.
DR Proteomes; UP000001600; Chromosome 2.
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 3D-structure; Carbohydrate metabolism; Magnesium; Metal-binding; NAD;
KW Nucleotide-binding; Oxidoreductase; Reference proteome.
FT CHAIN 1..345
FT /note="D-apiose dehydrogenase"
FT /id="PRO_0000446033"
FT BINDING 15..16
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 24
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 25
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 27
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 30
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 37
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 79
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 97..98
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 98
FT /ligand="substrate"
FT /evidence="ECO:0000305|Ref.3"
FT BINDING 126
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 165..167
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 165
FT /ligand="substrate"
FT /evidence="ECO:0000305|Ref.3"
FT BINDING 178
FT /ligand="substrate"
FT /evidence="ECO:0000305|Ref.3"
FT BINDING 182
FT /ligand="substrate"
FT /evidence="ECO:0000305|Ref.3"
FT BINDING 232
FT /ligand="substrate"
FT /evidence="ECO:0000305|Ref.3"
FT STRAND 6..11
FT /evidence="ECO:0007829|PDB:5UI9"
FT HELIX 17..26
FT /evidence="ECO:0007829|PDB:5UI9"
FT STRAND 30..36
FT /evidence="ECO:0007829|PDB:5UI9"
FT HELIX 40..50
FT /evidence="ECO:0007829|PDB:5UI9"
FT STRAND 54..58
FT /evidence="ECO:0007829|PDB:5UI9"
FT HELIX 59..65
FT /evidence="ECO:0007829|PDB:5UI9"
FT STRAND 69..73
FT /evidence="ECO:0007829|PDB:5UI9"
FT HELIX 77..79
FT /evidence="ECO:0007829|PDB:5UI9"
FT HELIX 80..89
FT /evidence="ECO:0007829|PDB:5UI9"
FT STRAND 94..99
FT /evidence="ECO:0007829|PDB:5UI9"
FT HELIX 104..116
FT /evidence="ECO:0007829|PDB:5UI9"
FT STRAND 121..124
FT /evidence="ECO:0007829|PDB:5UI9"
FT HELIX 127..129
FT /evidence="ECO:0007829|PDB:5UI9"
FT HELIX 131..141
FT /evidence="ECO:0007829|PDB:5UI9"
FT TURN 142..145
FT /evidence="ECO:0007829|PDB:5UI9"
FT STRAND 147..156
FT /evidence="ECO:0007829|PDB:5UI9"
FT TURN 161..164
FT /evidence="ECO:0007829|PDB:5UI9"
FT HELIX 166..169
FT /evidence="ECO:0007829|PDB:5UI9"
FT HELIX 175..178
FT /evidence="ECO:0007829|PDB:5UI9"
FT HELIX 180..191
FT /evidence="ECO:0007829|PDB:5UI9"
FT STRAND 194..202
FT /evidence="ECO:0007829|PDB:5UI9"
FT STRAND 208..210
FT /evidence="ECO:0007829|PDB:5UIB"
FT STRAND 213..220
FT /evidence="ECO:0007829|PDB:5UI9"
FT STRAND 225..232
FT /evidence="ECO:0007829|PDB:5UI9"
FT STRAND 245..250
FT /evidence="ECO:0007829|PDB:5UI9"
FT STRAND 253..258
FT /evidence="ECO:0007829|PDB:5UI9"
FT TURN 259..261
FT /evidence="ECO:0007829|PDB:5UI9"
FT STRAND 262..266
FT /evidence="ECO:0007829|PDB:5UI9"
FT STRAND 271..275
FT /evidence="ECO:0007829|PDB:5UI9"
FT TURN 286..288
FT /evidence="ECO:0007829|PDB:5UIA"
FT HELIX 289..308
FT /evidence="ECO:0007829|PDB:5UI9"
FT HELIX 316..335
FT /evidence="ECO:0007829|PDB:5UI9"
FT STRAND 339..341
FT /evidence="ECO:0007829|PDB:5UI9"
FT HELIX 342..344
FT /evidence="ECO:0007829|PDB:5UI9"
SQ SEQUENCE 345 AA; 37447 MW; 49BAB9B3CD69F1AF CRC64;
MNMTELKGAL IGCGFFAVNQ MHAWKDVKGA GIAAICDRDP KRLKLVGDQF GIERRYGDAA
ALFADGGFDF VDIATTVQSH RALVEMAAAH KVPAICQKPF AKSLSDAKAM VRTCENADIP
LMVHENFRWQ TPIQAVKAVL ESGAIGEPFW GRFSFRSGFD VFSGQPYLAE GERFIIEDLG
IHTLDIARFI LGDVATLTAR TKRVNPKIKG EDVATILLDH QNGATSIVDV SYATKLGTEP
FPETLIDIDG TQGTIRLSQG YRLEVTGPNG MTISDASPQL LSWASRPWHN IQESVLAIQQ
HWTDRLSSGG ETSTSGADNL KTFALVEAAY ESAANGRTVD IGAML
