ID   MTNA_ORYSJ              Reviewed;         374 AA.
AC   Q0ITU1; A0A0P0Y063; Q2R8T8;
DT   30-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT   03-OCT-2006, sequence version 1.
DT   03-AUG-2022, entry version 102.
DE   RecName: Full=Methylthioribose-1-phosphate isomerase {ECO:0000255|HAMAP-Rule:MF_03119};
DE            Short=M1Pi {ECO:0000255|HAMAP-Rule:MF_03119};
DE            Short=MTR-1-P isomerase {ECO:0000255|HAMAP-Rule:MF_03119};
DE            EC=5.3.1.23 {ECO:0000255|HAMAP-Rule:MF_03119};
DE   AltName: Full=Protein IRON DEFICIENCY INDUCIBLE 2;
DE            Short=OsIDI2;
DE   AltName: Full=S-methyl-5-thioribose-1-phosphate isomerase {ECO:0000255|HAMAP-Rule:MF_03119};
DE   AltName: Full=Translation initiation factor eIF-2B subunit alpha/beta/delta-like protein {ECO:0000255|HAMAP-Rule:MF_03119};
GN   Name=IDI2; OrderedLocusNames=Os11g0216900, LOC_Os11g11050;
GN   ORFNames=OsJ_33377;
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=16188032; DOI=10.1186/1741-7007-3-20;
RG   The rice chromosomes 11 and 12 sequencing consortia;
RT   "The sequence of rice chromosomes 11 and 12, rich in disease resistance
RT   genes and recent gene duplications.";
RL   BMC Biol. 3:20-20(2005).
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 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   [6]
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).
RN   [7]
RP   IDENTIFICATION, AND INDUCTION.
RX   PubMed=15781441; DOI=10.1093/jxb/eri131;
RA   Kobayashi T., Suzuki M., Inoue H., Itai R.N., Takahashi M., Nakanishi H.,
RA   Mori S., Nishizawa N.K.;
RT   "Expression of iron-acquisition-related genes in iron-deficient rice is co-
RT   ordinately induced by partially conserved iron-deficiency-responsive
RT   elements.";
RL   J. Exp. Bot. 56:1305-1316(2005).
CC   -!- FUNCTION: Catalyzes the interconversion of methylthioribose-1-phosphate
CC       (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).
CC       {ECO:0000255|HAMAP-Rule:MF_03119}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-
CC         D-ribulose 1-phosphate; Xref=Rhea:RHEA:19989, ChEBI:CHEBI:58533,
CC         ChEBI:CHEBI:58548; EC=5.3.1.23; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_03119};
CC   -!- PATHWAY: Amino-acid biosynthesis; L-methionine biosynthesis via salvage
CC       pathway; L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate:
CC       step 1/6. {ECO:0000255|HAMAP-Rule:MF_03119}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_03119}.
CC       Nucleus {ECO:0000255|HAMAP-Rule:MF_03119}.
CC   -!- INDUCTION: By iron deficiency in roots. {ECO:0000269|PubMed:15781441}.
CC   -!- SIMILARITY: Belongs to the eIF-2B alpha/beta/delta subunits family.
CC       MtnA subfamily. {ECO:0000255|HAMAP-Rule:MF_03119}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=ABA92066.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; DP000010; ABA92066.2; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP008217; BAF27874.1; -; Genomic_DNA.
DR   EMBL; AP014967; BAT13224.1; -; Genomic_DNA.
DR   EMBL; CM000148; EEE51856.1; -; Genomic_DNA.
DR   EMBL; AK060549; -; NOT_ANNOTATED_CDS; mRNA.
DR   EMBL; BR000390; FAA00313.1; -; mRNA.
DR   RefSeq; XP_015617957.1; XM_015762471.1.
DR   RefSeq; XP_015617958.1; XM_015762472.1.
DR   AlphaFoldDB; Q0ITU1; -.
DR   SMR; Q0ITU1; -.
DR   STRING; 4530.OS11T0216900-02; -.
DR   PaxDb; Q0ITU1; -.
DR   PRIDE; Q0ITU1; -.
DR   EnsemblPlants; Os11t0216900-01; Os11t0216900-01; Os11g0216900.
DR   EnsemblPlants; Os11t0216900-02; Os11t0216900-02; Os11g0216900.
DR   EnsemblPlants; Os11t0216900-03; Os11t0216900-03; Os11g0216900.
DR   GeneID; 4350083; -.
DR   Gramene; Os11t0216900-01; Os11t0216900-01; Os11g0216900.
DR   Gramene; Os11t0216900-02; Os11t0216900-02; Os11g0216900.
DR   Gramene; Os11t0216900-03; Os11t0216900-03; Os11g0216900.
DR   KEGG; osa:4350083; -.
DR   eggNOG; KOG1468; Eukaryota.
DR   HOGENOM; CLU_016218_1_3_1; -.
DR   InParanoid; Q0ITU1; -.
DR   OMA; RLWVDET; -.
DR   OrthoDB; 1410886at2759; -.
DR   PlantReactome; R-OSA-1119624; Methionine salvage pathway.
DR   UniPathway; UPA00904; UER00874.
DR   Proteomes; UP000000763; Chromosome 11.
DR   Proteomes; UP000007752; Chromosome 11.
DR   Proteomes; UP000059680; Chromosome 11.
DR   Genevisible; Q0ITU1; OS.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0046523; F:S-methyl-5-thioribose-1-phosphate isomerase activity; IBA:GO_Central.
DR   GO; GO:0019509; P:L-methionine salvage from methylthioadenosine; IBA:GO_Central.
DR   GO; GO:0019284; P:L-methionine salvage from S-adenosylmethionine; IEA:UniProtKB-UniRule.
DR   Gene3D; 1.20.120.420; -; 1.
DR   Gene3D; 3.40.50.10470; -; 1.
DR   HAMAP; MF_01678; Salvage_MtnA; 1.
DR   InterPro; IPR000649; IF-2B-related.
DR   InterPro; IPR005251; IF-M1Pi.
DR   InterPro; IPR042529; IF_2B-like_C.
DR   InterPro; IPR011559; Initiation_fac_2B_a/b/d.
DR   InterPro; IPR027363; M1Pi_N.
DR   InterPro; IPR037171; NagB/RpiA_transferase-like.
DR   Pfam; PF01008; IF-2B; 1.
DR   SUPFAM; SSF100950; SSF100950; 1.
DR   TIGRFAMs; TIGR00524; eIF-2B_rel; 1.
DR   TIGRFAMs; TIGR00512; salvage_mtnA; 1.
PE   2: Evidence at transcript level;
KW   Amino-acid biosynthesis; Cytoplasm; Isomerase; Methionine biosynthesis;
KW   Nucleus; Reference proteome.
FT   CHAIN           1..374
FT                   /note="Methylthioribose-1-phosphate isomerase"
FT                   /id="PRO_0000401993"
FT   ACT_SITE        251
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03119"
FT   SITE            171
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03119"
SQ   SEQUENCE   374 AA;  39508 MW;  24CDB242BEBA6C1C CRC64;
     MGELGALQSI VYHRGSLRLL DQRKLPLEVD YIDVKCSGDG WNAIRDMVVR GAPAIAIAAA
     LALAVEVSGL EDFTGTPAEA AVFVSEKLEY LVSSRPTAVN LSDAATKLRS LVSRTAETEK
     DAKAIFQAYI DAAETMLVDD VSDNKAIGSH GAEFLKQKLE VSKDISVLTH CNTGSLATAG
     YGTALGVIRA LHSGGILEKA FCTETRPFNQ GSRLTAFELV HDKVPATLIA DSAAAALMKS
     GCIQAVIVGA DRIAANGDTA NKIGTYNLAI SAKHHGVQFY VAAPITSIDL SLPSGEQIVI
     EERSPNELLN SEGGLGKQVA ASGISVWNPA FDVTPANLIT AIITEKGVIT KSDADETFNI
     KDFIQSAKLY STMQ