PANB1_ORYSJ
ID PANB1_ORYSJ Reviewed; 364 AA.
AC Q9AWZ8; Q0JPF4;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 118.
DE RecName: Full=3-methyl-2-oxobutanoate hydroxymethyltransferase 1, mitochondrial;
DE EC=2.1.2.11;
DE AltName: Full=Ketopantoate hydroxymethyltransferase 1;
DE Flags: Precursor;
GN Name=KPHMT1; Synonyms=PANB1;
GN OrderedLocusNames=Os01g0225400, LOC_Os01g12560;
GN ORFNames=P0443E07.6, P0492F05.15;
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=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
RN [2]
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 [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RG The rice full-length cDNA consortium;
RT "Oryza sativa full length cDNA.";
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the reversible reaction in which hydroxymethyl
CC group from 5,10-methylenetetrahydrofolate is transferred onto alpha-
CC ketoisovalerate to form ketopantoate. {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + 3-methyl-2-
CC oxobutanoate + H2O = (6S)-5,6,7,8-tetrahydrofolate + 2-
CC dehydropantoate; Xref=Rhea:RHEA:11824, ChEBI:CHEBI:11561,
CC ChEBI:CHEBI:11851, ChEBI:CHEBI:15377, ChEBI:CHEBI:15636,
CC ChEBI:CHEBI:57453; EC=2.1.2.11;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000250};
CC -!- PATHWAY: Cofactor biosynthesis; (R)-pantothenate biosynthesis; (R)-
CC pantoate from 3-methyl-2-oxobutanoate: step 1/2.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the PanB family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF04374.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP002900; BAB92103.1; -; Genomic_DNA.
DR EMBL; AP002902; BAB32712.1; -; Genomic_DNA.
DR EMBL; AP008207; BAF04374.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014957; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AK242525; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015629790.1; XM_015774304.1.
DR AlphaFoldDB; Q9AWZ8; -.
DR SMR; Q9AWZ8; -.
DR STRING; 4530.OS01T0225400-01; -.
DR PaxDb; Q9AWZ8; -.
DR PRIDE; Q9AWZ8; -.
DR GeneID; 4326739; -.
DR KEGG; osa:4326739; -.
DR eggNOG; KOG2949; Eukaryota.
DR InParanoid; Q9AWZ8; -.
DR OrthoDB; 1439584at2759; -.
DR PlantReactome; R-OSA-1119496; Pantothenate biosynthesis I.
DR PlantReactome; R-OSA-1119544; Pantothenate biosynthesis II.
DR UniPathway; UPA00028; UER00003.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0003864; F:3-methyl-2-oxobutanoate hydroxymethyltransferase activity; IBA:GO_Central.
DR GO; GO:0000287; F:magnesium ion binding; IBA:GO_Central.
DR GO; GO:0015940; P:pantothenate biosynthetic process; IBA:GO_Central.
DR CDD; cd06557; KPHMT-like; 1.
DR Gene3D; 3.20.20.60; -; 1.
DR HAMAP; MF_00156; PanB; 1.
DR InterPro; IPR003700; Pantoate_hydroxy_MeTrfase.
DR InterPro; IPR015813; Pyrv/PenolPyrv_Kinase-like_dom.
DR InterPro; IPR040442; Pyrv_Kinase-like_dom_sf.
DR PANTHER; PTHR20881; PTHR20881; 1.
DR Pfam; PF02548; Pantoate_transf; 1.
DR SUPFAM; SSF51621; SSF51621; 1.
DR TIGRFAMs; TIGR00222; panB; 1.
PE 2: Evidence at transcript level;
KW Magnesium; Metal-binding; Mitochondrion; Pantothenate biosynthesis;
KW Reference proteome; Transferase; Transit peptide.
FT TRANSIT 1..59
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 60..364
FT /note="3-methyl-2-oxobutanoate hydroxymethyltransferase 1,
FT mitochondrial"
FT /id="PRO_0000429568"
FT ACT_SITE 233
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 94..95
FT /ligand="3-methyl-2-oxobutanoate"
FT /ligand_id="ChEBI:CHEBI:11851"
FT /evidence="ECO:0000250"
FT BINDING 94
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 133
FT /ligand="3-methyl-2-oxobutanoate"
FT /ligand_id="ChEBI:CHEBI:11851"
FT /evidence="ECO:0000250"
FT BINDING 133
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 163
FT /ligand="3-methyl-2-oxobutanoate"
FT /ligand_id="ChEBI:CHEBI:11851"
FT /evidence="ECO:0000250"
FT BINDING 165
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT CONFLICT 321
FT /note="Y -> F (in Ref. 5; AK242525)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 364 AA; 37921 MW; 3393C0A29F2B1512 CRC64;
MMMMMRRAFR HLARQQRRPL SHVPESAVYG GPRPQDVGAA AGAGAGAGAT RRVTVTTLRG
KHRRGEPITV VTAYDYPSAV HVDSAGIDVC LVGDSAAMVV HGHDTTLPIS LDVMLEHCRA
VARGATRPLL VGDLPFGCYE SSSTRAVDSA VRVLKEGGMD AIKLEGGAPS RISAAKAIVE
AGIAVMGHVG LTPQAISVLG GFRPQGKTVD SAVKVVETAL ALQEAGCFSV VLECVPAPVA
AAATSALQIP TIGIGAGPFC SGQVLVYHDL LGMMQHPHHA KVTPKFCKQF GNVGHVINKA
LSEYKQEVET RSFPGPSHTP YKIAAADVDG FANALQKMGL DEAANAAAAA AENAEKDGEL
PENK
