BIODA_ORYSJ
ID BIODA_ORYSJ Reviewed; 821 AA.
AC Q6ZKV8; A0A0P0XDC2;
DT 13-JUN-2012, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial;
DE AltName: Full=Bifunctional BIO3-BIO1 protein;
DE Includes:
DE RecName: Full=Dethiobiotin synthetase;
DE EC=6.3.3.3;
DE AltName: Full=DTB synthetase;
DE Short=DTBS;
DE AltName: Full=Protein BIOTIN AUXOTROPH 3;
DE Includes:
DE RecName: Full=7,8-diamino-pelargonic acid aminotransferase;
DE Short=DAPA AT;
DE Short=DAPA aminotransferase;
DE AltName: Full=7,8-diaminononanoate synthase;
DE Short=DANS;
DE AltName: Full=Adenosylmethionine-8-amino-7-oxononanoate aminotransferase;
DE EC=2.6.1.62;
DE AltName: Full=Diaminopelargonic acid synthase;
DE AltName: Full=Protein BIOTIN AUXOTROPH 1;
DE Flags: Precursor;
GN Name=BIO3-BIO1; Synonyms=BIO1, BIO3;
GN OrderedLocusNames=Os08g0245400, LOC_Os08g14770;
GN ORFNames=OJ1033_B09.17, OsJ_26590;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
CC -!- FUNCTION: Bifunctional enzyme that catalyzes two different reactions
CC involved in the biotin biosynthesis.
CC -!- FUNCTION: Catalyzes a mechanistically unusual reaction, the ATP-
CC dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-
CC diaminopelargonic acid (DAPA) to form an ureido ring. {ECO:0000250}.
CC -!- FUNCTION: Catalyzes the transfer of the alpha-amino group from S-
CC adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to
CC form 7,8-diaminopelargonic acid (DAPA). It is the only aminotransferase
CC known to utilize SAM as an amino donor (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(7R,8S)-7,8-diammoniononanoate + ATP + CO2 = (4R,5S)-
CC dethiobiotin + ADP + 3 H(+) + phosphate; Xref=Rhea:RHEA:15805,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:149469, ChEBI:CHEBI:149473,
CC ChEBI:CHEBI:456216; EC=6.3.3.3;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(8S)-8-amino-7-oxononanoate + S-adenosyl-L-methionine =
CC (7R,8S)-7,8-diammoniononanoate + S-adenosyl-4-methylsulfanyl-2-
CC oxobutanoate; Xref=Rhea:RHEA:16861, ChEBI:CHEBI:16490,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:149468, ChEBI:CHEBI:149469;
CC EC=2.6.1.62;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000250};
CC -!- PATHWAY: Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-
CC diaminononanoate: step 1/2.
CC -!- PATHWAY: Cofactor biosynthesis; biotin biosynthesis; 7,8-
CC diaminononanoate from 8-amino-7-oxononanoate (SAM route): step 1/1.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000305}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the dethiobiotin
CC synthetase family. {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the class-III
CC pyridoxal-phosphate-dependent aminotransferase family. BioA subfamily.
CC {ECO:0000305}.
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DR EMBL; AP003859; BAD05190.1; -; Genomic_DNA.
DR EMBL; AP008214; BAF23268.1; -; Genomic_DNA.
DR EMBL; AP014964; BAT04525.1; -; Genomic_DNA.
DR EMBL; CM000145; EEE68317.1; -; Genomic_DNA.
DR EMBL; AK100945; BAG94844.1; -; mRNA.
DR RefSeq; XP_015650723.1; XM_015795237.1.
DR AlphaFoldDB; Q6ZKV8; -.
DR SMR; Q6ZKV8; -.
DR STRING; 4530.OS08T0245400-01; -.
DR PaxDb; Q6ZKV8; -.
DR PRIDE; Q6ZKV8; -.
DR EnsemblPlants; Os08t0245400-01; Os08t0245400-01; Os08g0245400.
DR GeneID; 4345056; -.
DR Gramene; Os08t0245400-01; Os08t0245400-01; Os08g0245400.
DR KEGG; osa:4345056; -.
DR eggNOG; KOG1401; Eukaryota.
DR HOGENOM; CLU_010794_0_0_1; -.
DR InParanoid; Q6ZKV8; -.
DR OMA; KGWASRA; -.
DR OrthoDB; 289012at2759; -.
DR PlantReactome; R-OSA-1119610; Biotin biosynthesis II.
DR UniPathway; UPA00078; UER00160.
DR UniPathway; UPA00078; UER00161.
DR Proteomes; UP000000763; Chromosome 8.
DR Proteomes; UP000007752; Chromosome 8.
DR Proteomes; UP000059680; Chromosome 8.
DR Genevisible; Q6ZKV8; OS.
DR GO; GO:0005759; C:mitochondrial matrix; IEA:EnsemblPlants.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0004015; F:adenosylmethionine-8-amino-7-oxononanoate transaminase activity; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004141; F:dethiobiotin synthase activity; IBA:GO_Central.
DR GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR GO; GO:0042803; F:protein homodimerization activity; IEA:EnsemblPlants.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0009102; P:biotin biosynthetic process; IBA:GO_Central.
DR Gene3D; 3.40.50.300; -; 1.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR HAMAP; MF_00336; BioD; 1.
DR InterPro; IPR005814; Aminotrans_3.
DR InterPro; IPR004472; DTB_synth_BioD.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR Pfam; PF00202; Aminotran_3; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR PROSITE; PS00600; AA_TRANSFER_CLASS_3; 1.
PE 2: Evidence at transcript level;
KW Aminotransferase; ATP-binding; Biotin biosynthesis; Ligase; Magnesium;
KW Metal-binding; Mitochondrion; Multifunctional enzyme; Nucleotide-binding;
KW Pyridoxal phosphate; Reference proteome; S-adenosyl-L-methionine;
KW Transferase; Transit peptide.
FT TRANSIT 1..?
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN ?..821
FT /note="Bifunctional dethiobiotin synthetase/7,8-diamino-
FT pelargonic acid aminotransferase, mitochondrial"
FT /id="PRO_0000417697"
FT REGION 28..283
FT /note="Dethiobiotin synthetase"
FT REGION 316..820
FT /note="7,8-diamino-pelargonic acid aminotransferase"
FT BINDING 39..44
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 43
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 72
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 194..197
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 194
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 374..375
FT /ligand="(8S)-8-amino-7-oxononanoate"
FT /ligand_id="ChEBI:CHEBI:149468"
FT /evidence="ECO:0000250"
FT BINDING 436..437
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 482
FT /ligand="(8S)-8-amino-7-oxononanoate"
FT /ligand_id="ChEBI:CHEBI:149468"
FT /evidence="ECO:0000250"
FT BINDING 626
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 655
FT /ligand="(8S)-8-amino-7-oxononanoate"
FT /ligand_id="ChEBI:CHEBI:149468"
FT /evidence="ECO:0000250"
FT BINDING 689
FT /ligand="(8S)-8-amino-7-oxononanoate"
FT /ligand_id="ChEBI:CHEBI:149468"
FT /evidence="ECO:0000250"
FT BINDING 691
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 787
FT /ligand="(8S)-8-amino-7-oxononanoate"
FT /ligand_id="ChEBI:CHEBI:149468"
FT /evidence="ECO:0000250"
FT SITE 332
FT /note="Participates in the substrate recognition with KAPA
FT and in a stacking interaction with the adenine ring of SAM"
FT /evidence="ECO:0000250"
FT MOD_RES 655
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
SQ SEQUENCE 821 AA; 90048 MW; 40663C38B8859EEE CRC64;
MLRLLRHARR HSTSSSSSAA AAAVPLTSPA FAVFGANTGV GKTLVSAGLV ASLLASPSPS
PSTVAYLKPL QTGFPDDSDA RFVFDRAPAL LRRLRLAGGG ASTRLVASNH TLFPSPAVDP
LPERQDTVVN YGGEEGVEEK ALVCRTVYAW REPVSPHLAA EREGMPVEDE EVRWLVDRWL
AEEDGGGEVW KVLETAGGVA SPGPSGTLQC DLYRSSRLPA VLVGDGRLGG ISSTLSAYET
LLLRGYDVGS VILEDRGLSN DRFLLSYLRK RVPVHVLPPI PEDPKDDLTD WFSESSSAFS
SLKDSLQSFH SRRVQRLNSM QRKSKYLLWW PFTQHDLVPV DSVTVIDSRF GENFSAYKVK
DKTIVPQFDA CASWWTQGPD SNLQIELARD MGYAAARYGH VMFPENVHEP ALRCAELLLG
GVGKDWASRV YFSDNGSTAI EIALKMAFRK YACDHGIIVD SEKDIRSEGS VHFKVLALNG
SYHGDTLGAM EAQAPSAYTS FLQQPWYSGR GLFLDPPTVY IKNKSANLSL PPSIMHDQLS
SCDTCFSSLT EVFCKTRDTS SAANVYVSYI SQQLSQYAMS NNSEHIAALI IEPVIQGAGG
MHLIDPLFQR LLVKECKNRK IPVIFDEVFT GFWRLGVESA SELLGCFPDI SCYAKLMTGG
IVPLAATLAT EPIFEAFRSD SKLTALLHGH SYTAHPMGCT AAVKAIQWYK DPSTNSNIDL
DRMKLKELWD SALVNHLSSL PNVKRVVSLG TLCAIELKAE GSDAGYASLY ASSLIRQLRE
EDNIYARPLG NVIYLMCGPC TTQDSCTRQL AKVHRRLQKL N
