ISPH_ARATH
ID ISPH_ARATH Reviewed; 466 AA.
AC Q94B35; B9DHZ9; Q56WI5; Q5EGH0; Q9SZ00;
DT 13-JUN-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=4-hydroxy-3-methylbut-2-enyl diphosphate reductase, chloroplastic {ECO:0000305};
DE EC=1.17.7.4 {ECO:0000305|PubMed:15863698};
DE AltName: Full=Protein CHLOROPLAST BIOGENESIS 6 {ECO:0000303|PubMed:15659625};
DE Flags: Precursor;
GN Name=ISPH {ECO:0000303|PubMed:15863698};
GN Synonyms=CLB6 {ECO:0000303|PubMed:15659625}, HDR {ECO:0000305};
GN OrderedLocusNames=At4g34350 {ECO:0000312|Araport:AT4G34350};
GN ORFNames=F10M10.120 {ECO:0000312|EMBL:CAB36712.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=15659625; DOI=10.1105/tpc.104.028860;
RA Guevara-Garcia A., San Roman C., Arroyo A., Cortes M.E.,
RA de la Luz Gutierrez-Nava M., Leon P.;
RT "Characterization of the Arabidopsis clb6 mutant illustrates the importance
RT of posttranscriptional regulation of the methyl-D-erythritol 4-phosphate
RT pathway.";
RL Plant Cell 17:628-643(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, TISSUE
RP SPECIFICITY, INDUCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=15863698; DOI=10.1104/pp.104.058735;
RA Hsieh M.H., Goodman H.M.;
RT "The Arabidopsis IspH homolog is involved in the plastid nonmevalonate
RT pathway of isoprenoid biosynthesis.";
RL Plant Physiol. 138:641-653(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 109-466.
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 247-466.
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [8]
RP SUBCELLULAR LOCATION.
RX PubMed=18236010; DOI=10.1007/s11103-008-9297-5;
RA Hsieh M.H., Chang C.Y., Hsu S.J., Chen J.J.;
RT "Chloroplast localization of methylerythritol 4-phosphate pathway enzymes
RT and regulation of mitochondrial genes in ispD and ispE albino mutants in
RT Arabidopsis.";
RL Plant Mol. Biol. 66:663-673(2008).
CC -!- FUNCTION: Enzyme of the plastid non-mevalonate pathway for isoprenoid
CC biosynthesis that converts 1-hydroxy-2-methyl-2-(E)-butenyl 4-
CC diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl
CC diphosphate (DMAPP). Is essential for chloroplast development.
CC {ECO:0000269|PubMed:15659625, ECO:0000269|PubMed:15863698}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-
CC [ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+)
CC + 2 reduced [2Fe-2S]-[ferredoxin]; Xref=Rhea:RHEA:24488, Rhea:RHEA-
CC COMP:10000, Rhea:RHEA-COMP:10001, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738,
CC ChEBI:CHEBI:128753, ChEBI:CHEBI:128769; EC=1.17.7.4;
CC Evidence={ECO:0000305|PubMed:15863698};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-
CC [ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+)
CC + 2 reduced [2Fe-2S]-[ferredoxin]; Xref=Rhea:RHEA:24825, Rhea:RHEA-
CC COMP:10000, Rhea:RHEA-COMP:10001, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738,
CC ChEBI:CHEBI:57623, ChEBI:CHEBI:128753; EC=1.17.7.4;
CC Evidence={ECO:0000305|PubMed:15863698};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000250|UniProtKB:P62623};
CC Note=Binds 1 [4Fe-4S] cluster per subunit.
CC {ECO:0000250|UniProtKB:P62623};
CC -!- PATHWAY: Isoprenoid biosynthesis; dimethylallyl diphosphate
CC biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-
CC methylbutenyl diphosphate: step 1/1. {ECO:0000305|PubMed:15863698}.
CC -!- PATHWAY: Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis
CC via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-
CC phosphate: step 6/6. {ECO:0000305|PubMed:15863698}.
CC -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:P62623}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:18236010}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, stems, leaves, flowers and
CC siliques. {ECO:0000269|PubMed:15863698}.
CC -!- INDUCTION: Circadian-regulated with a peak in the late period of dark
CC phase and early period of the light phase.
CC {ECO:0000269|PubMed:15863698}.
CC -!- DISRUPTION PHENOTYPE: Albino phenotype and seedling lethal when
CC homozygous. The phenotype is caused by an early arrest in chloroplast
CC differentiation. {ECO:0000269|PubMed:15659625,
CC ECO:0000269|PubMed:15863698}.
CC -!- SIMILARITY: Belongs to the IspH family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAW82381.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAD94833.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAB36712.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB80152.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AY883838; AAW82381.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AY168881; AAN87171.1; -; mRNA.
DR EMBL; AL035521; CAB36712.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161585; CAB80152.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE86362.1; -; Genomic_DNA.
DR EMBL; AY042877; AAK68817.1; -; mRNA.
DR EMBL; AY081454; AAM10016.1; -; mRNA.
DR EMBL; AK317707; BAH20366.1; -; mRNA.
DR EMBL; AK222055; BAD94833.1; ALT_INIT; mRNA.
DR PIR; T04781; T04781.
DR RefSeq; NP_567965.1; NM_119600.4.
DR AlphaFoldDB; Q94B35; -.
DR SMR; Q94B35; -.
DR STRING; 3702.AT4G34350.1; -.
DR MetOSite; Q94B35; -.
DR PaxDb; Q94B35; -.
DR PRIDE; Q94B35; -.
DR ProteomicsDB; 232230; -.
DR EnsemblPlants; AT4G34350.1; AT4G34350.1; AT4G34350.
DR GeneID; 829585; -.
DR Gramene; AT4G34350.1; AT4G34350.1; AT4G34350.
DR KEGG; ath:AT4G34350; -.
DR Araport; AT4G34350; -.
DR TAIR; locus:2116164; AT4G34350.
DR eggNOG; ENOG502QPIQ; Eukaryota.
DR HOGENOM; CLU_027486_4_1_1; -.
DR InParanoid; Q94B35; -.
DR OMA; QSASFIV; -.
DR OrthoDB; 1067589at2759; -.
DR PhylomeDB; Q94B35; -.
DR BioCyc; ARA:AT4G34350-MON-9581; -.
DR BioCyc; MetaCyc:AT4G34350-MON-9581; -.
DR BRENDA; 1.17.7.4; 399.
DR UniPathway; UPA00056; UER00097.
DR UniPathway; UPA00059; UER00105.
DR PRO; PR:Q94B35; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q94B35; baseline and differential.
DR Genevisible; Q94B35; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; IDA:TAIR.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0051745; F:4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity; IEA:UniProtKB-EC.
DR GO; GO:0046429; F:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity; IMP:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0050992; P:dimethylallyl diphosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0019288; P:isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway; IEP:TAIR.
DR CDD; cd13944; lytB_ispH; 1.
DR HAMAP; MF_00191; IspH; 1.
DR InterPro; IPR003451; LytB/IspH.
DR Pfam; PF02401; LYTB; 1.
DR TIGRFAMs; TIGR00216; ispH_lytB; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Chloroplast; Iron; Iron-sulfur; Isoprene biosynthesis;
KW Metal-binding; Oxidoreductase; Plastid; Reference proteome;
KW Transit peptide.
FT TRANSIT 1..38
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 39..466
FT /note="4-hydroxy-3-methylbut-2-enyl diphosphate reductase,
FT chloroplastic"
FT /id="PRO_0000417592"
FT ACT_SITE 243
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P62623"
FT BINDING 122
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P62623"
FT BINDING 152
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62623"
FT BINDING 213
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P62623"
FT BINDING 241
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62623"
FT BINDING 312
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62623"
FT BINDING 350
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P62623"
FT BINDING 379..381
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62623"
FT BINDING 441
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62623"
SQ SEQUENCE 466 AA; 52781 MW; B008808517890DC6 CRC64;
MAVALQFSRL CVRPDTFVRE NHLSGSGSLR RRKALSVRCS SGDENAPSPS VVMDSDFDAK
VFRKNLTRSD NYNRKGFGHK EETLKLMNRE YTSDILETLK TNGYTYSWGD VTVKLAKAYG
FCWGVERAVQ IAYEARKQFP EERLWITNEI IHNPTVNKRL EDMDVKIIPV EDSKKQFDVV
EKDDVVILPA FGAGVDEMYV LNDKKVQIVD TTCPWVTKVW NTVEKHKKGE YTSVIHGKYN
HEETIATASF AGKYIIVKNM KEANYVCDYI LGGQYDGSSS TKEEFMEKFK YAISKGFDPD
NDLVKVGIAN QTTMLKGETE EIGRLLETTM MRKYGVENVS GHFISFNTIC DATQERQDAI
YELVEEKIDL MLVVGGWNSS NTSHLQEISE ARGIPSYWID SEKRIGPGNK IAYKLHYGEL
VEKENFLPKG PITIGVTSGA STPDKVVEDA LVKVFDIKRE ELLQLA
