PHYLO_ARATH
ID PHYLO_ARATH Reviewed; 1715 AA.
AC Q15KI9; Q0WV21; Q15KJ0; Q9CAB1; Q9CAB2;
DT 05-APR-2011, integrated into UniProtKB/Swiss-Prot.
DT 27-JUL-2011, sequence version 2.
DT 03-AUG-2022, entry version 111.
DE RecName: Full=Protein PHYLLO, chloroplastic;
DE Includes:
DE RecName: Full=Inactive isochorismate synthase;
DE AltName: Full=MENF;
DE Includes:
DE RecName: Full=2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase;
DE EC=2.2.1.9;
DE AltName: Full=MEND;
DE Includes:
DE RecName: Full=o-succinylbenzoate synthase;
DE EC=4.2.1.113;
DE AltName: Full=MENC;
DE Includes:
DE RecName: Full=2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase;
DE EC=4.2.99.20;
DE AltName: Full=MENH;
DE Flags: Precursor;
GN Name=PHYLLO; OrderedLocusNames=At1g68890/At1g68900; ORFNames=T6L1.7/T6L1.8;
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 [MRNA] (ISOFORMS 1 AND 2), ALTERNATIVE SPLICING,
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=16617180; DOI=10.1074/jbc.m601754200;
RA Gross J., Cho W.K., Lezhneva L., Falk J., Krupinska K., Shinozaki K.,
RA Seki M., Herrmann R.G., Meurer J.;
RT "A plant locus essential for phylloquinone (vitamin K1) biosynthesis
RT originated from a fusion of four eubacterial genes.";
RL J. Biol. Chem. 281:17189-17196(2006).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 345-1715 (ISOFORM 1).
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Morosawa T.,
RA Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K.,
RA Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K.,
RA Akiyama K., Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J.,
RA Hayashizaki Y., Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Multifunctional enzyme required for phylloquinone (vitamin
CC K1) biosynthesis. {ECO:0000269|PubMed:16617180}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + H(+) + isochorismate = 5-enolpyruvoyl-6-
CC hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate + CO2;
CC Xref=Rhea:RHEA:25593, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:29780, ChEBI:CHEBI:58818; EC=2.2.1.9;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate
CC = 2-succinylbenzoate + H2O; Xref=Rhea:RHEA:10196, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:18325, ChEBI:CHEBI:58689; EC=4.2.1.113;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-
CC carboxylate = (1R,6R)-6-hydroxy-2-succinyl-cyclohexa-2,4-diene-1-
CC carboxylate + pyruvate; Xref=Rhea:RHEA:25597, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:58689, ChEBI:CHEBI:58818; EC=4.2.99.20;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC -!- COFACTOR:
CC Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
CC Evidence={ECO:0000250};
CC Note=Binds 1 thiamine pyrophosphate per subunit. {ECO:0000250};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast membrane {ECO:0000305};
CC Single-pass membrane protein {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q15KI9-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q15KI9-2; Sequence=VSP_040862, VSP_040863;
CC -!- DISRUPTION PHENOTYPE: High chlorophyll fluorescence and lack of
CC phylloquinone. {ECO:0000269|PubMed:16617180}.
CC -!- MISCELLANEOUS: Consists of a fusion of four bacterial genes, menF,
CC menD, menC and menH belonging to the same operon. In higher plants, the
CC C-terminal chorismate binding domain is absent from the isochorismate
CC synthase (MenF) module, leading to a non-functional module. The
CC isochorismate synthase activity has been taken over by ISC1 and ICS2.
CC In green and red algae lineages, this module has maintained its
CC structural integrity and is functional (PubMed:16617180).
CC {ECO:0000305|PubMed:16617180}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the isochorismate
CC synthase family. {ECO:0000305}.
CC -!- SIMILARITY: In the 2nd section; belongs to the TPP enzyme family. MenD
CC subfamily. {ECO:0000305}.
CC -!- SIMILARITY: In the 3rd section; belongs to the mandelate
CC racemase/muconate lactonizing enzyme family. MenC type 1 subfamily.
CC {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the AB hydrolase
CC superfamily. MenH family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG51591.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At1g68890 and At1g68900.; Evidence={ECO:0000305};
CC Sequence=AAG51593.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At1g68890 and At1g68900.; Evidence={ECO:0000305};
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DR EMBL; DQ084385; AAZ40194.1; -; mRNA.
DR EMBL; DQ084386; AAZ40195.1; -; mRNA.
DR EMBL; AC011665; AAG51591.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC011665; AAG51593.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE34855.1; -; Genomic_DNA.
DR EMBL; AK226959; BAE99027.1; -; mRNA.
DR PIR; D96713; D96713.
DR PIR; E96713; E96713.
DR RefSeq; NP_001322314.1; NM_001334389.1.
DR RefSeq; NP_177055.2; NM_105563.5. [Q15KI9-1]
DR AlphaFoldDB; Q15KI9; -.
DR SMR; Q15KI9; -.
DR STRING; 3702.AT1G68890.1; -.
DR ESTHER; arath-T6L1.8; MenH_SHCHC.
DR MEROPS; S33.A36; -.
DR PaxDb; Q15KI9; -.
DR PRIDE; Q15KI9; -.
DR ProteomicsDB; 234723; -. [Q15KI9-1]
DR EnsemblPlants; AT1G68890.1; AT1G68890.1; AT1G68890. [Q15KI9-1]
DR GeneID; 843222; -.
DR Gramene; AT1G68890.1; AT1G68890.1; AT1G68890. [Q15KI9-1]
DR KEGG; ath:AT1G68890; -.
DR Araport; AT1G68890; -.
DR TAIR; locus:2205450; AT1G68890.
DR eggNOG; KOG1223; Eukaryota.
DR eggNOG; KOG2382; Eukaryota.
DR HOGENOM; CLU_001622_0_0_1; -.
DR InParanoid; Q15KI9; -.
DR OrthoDB; 38394at2759; -.
DR BioCyc; ARA:AT1G68890-MON; -.
DR BioCyc; MetaCyc:AT1G68890-MON; -.
DR PRO; PR:Q15KI9; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q15KI9; baseline and differential.
DR Genevisible; Q15KI9; AT.
DR GO; GO:0031969; C:chloroplast membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0070204; F:2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0070205; F:2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0043748; F:O-succinylbenzoate synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IEA:InterPro.
DR GO; GO:0009063; P:cellular amino acid catabolic process; IEA:InterPro.
DR GO; GO:0009234; P:menaquinone biosynthetic process; IEA:InterPro.
DR GO; GO:0042550; P:photosystem I stabilization; IMP:TAIR.
DR GO; GO:0042372; P:phylloquinone biosynthetic process; IMP:TAIR.
DR Gene3D; 3.20.20.120; -; 1.
DR Gene3D; 3.30.390.10; -; 1.
DR Gene3D; 3.40.50.1820; -; 1.
DR HAMAP; MF_01659; MenD; 1.
DR InterPro; IPR029058; AB_hydrolase.
DR InterPro; IPR000073; AB_hydrolase_1.
DR InterPro; IPR029035; DHS-like_NAD/FAD-binding_dom.
DR InterPro; IPR036849; Enolase-like_C_sf.
DR InterPro; IPR029017; Enolase-like_N.
DR InterPro; IPR029065; Enolase_C-like.
DR InterPro; IPR018110; Mandel_Rmase/mucon_lact_enz_CS.
DR InterPro; IPR013342; Mandelate_racemase_C.
DR InterPro; IPR004433; MenaQ_synth_MenD.
DR InterPro; IPR032264; MenD_middle.
DR InterPro; IPR029061; THDP-binding.
DR InterPro; IPR012001; Thiamin_PyroP_enz_TPP-bd_dom.
DR InterPro; IPR011766; TPP_enzyme-bd_C.
DR PANTHER; PTHR42916; PTHR42916; 1.
DR Pfam; PF00561; Abhydrolase_1; 1.
DR Pfam; PF13378; MR_MLE_C; 1.
DR Pfam; PF02775; TPP_enzyme_C; 1.
DR Pfam; PF16582; TPP_enzyme_M_2; 1.
DR Pfam; PF02776; TPP_enzyme_N; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; SSF51604; 1.
DR SUPFAM; SSF52467; SSF52467; 1.
DR SUPFAM; SSF52518; SSF52518; 2.
DR SUPFAM; SSF53474; SSF53474; 1.
DR SUPFAM; SSF54826; SSF54826; 1.
DR TIGRFAMs; TIGR00173; menD; 1.
DR PROSITE; PS00909; MR_MLE_2; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Chloroplast; Lyase; Magnesium; Manganese; Membrane;
KW Metal-binding; Multifunctional enzyme; Plastid; Reference proteome;
KW Thiamine pyrophosphate; Transferase; Transit peptide; Transmembrane;
KW Transmembrane helix.
FT TRANSIT 1..19
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 20..1715
FT /note="Protein PHYLLO, chloroplastic"
FT /id="PRO_0000406882"
FT TRANSMEM 429..449
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 1435..1540
FT /note="AB hydrolase-1"
FT /evidence="ECO:0000255"
FT REGION 20..273
FT /note="Inactive isochorismate synthase"
FT /evidence="ECO:0000250"
FT REGION 363..933
FT /note="2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-
FT carboxylate synthase"
FT /evidence="ECO:0000250"
FT REGION 981..1364
FT /note="O-succinylbenzoate synthase"
FT /evidence="ECO:0000250"
FT REGION 1418..1715
FT /note="2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-
FT carboxylate synthase"
FT /evidence="ECO:0000250"
FT ACT_SITE 1170
FT /note="Proton donor; for the o-succinylbenzoate synthase
FT activity"
FT /evidence="ECO:0000250"
FT ACT_SITE 1279
FT /note="Proton acceptor; for the o-succinylbenzoate synthase
FT activity"
FT /evidence="ECO:0000250"
FT BINDING 1202
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1228
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 1251
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT VAR_SEQ 323..327
FT /note="KSIQS -> VSSLP (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16617180"
FT /id="VSP_040862"
FT VAR_SEQ 328..1715
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16617180"
FT /id="VSP_040863"
FT CONFLICT 48
FT /note="R -> Q (in Ref. 1; AAZ40194/AAZ40195)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1715 AA; 190182 MW; A88CB4B483685950 CRC64;
MRSSFLVSNP PFLPSLIPRY SSRKSIRRSR ERFSFPESLR VSLLHGIRRN IEVAQGVQFD
GPIMDRDVNL DDDLVVQVCV TRTLPPALTL ELGLESLKEA IDELKTNPPK SSSGVLRFQV
AVPPRAKALF WFCSQPTTSD VFPVFFLSKD TVEPSYKSLY VKEPHGVFGI GNAFAFVHSS
SVDSNGHSMI KTFLSDESAM VTAYGFPDIE FNKYSTVNSK DGSSYFFVPQ IELDEHEEVS
ILAVTLAWNE SLSYTVEQTI SSYEKSIFQV SSHFCPNVED HWFKHLKSSL AKLSVEEIHP
LEMEHMGFFT FSGRDQADVK ELKSIQSSCQ FHCKLSPDVV FSNNMLNRET EVSNFLRDEA
NINAVWASAI IEECTRLGLT YFCVAPGSRS SHLAIAAANH PLTTCLACFD ERSLAFHAIG
YAKGSLKPAV IITSSGTAVS NLLPAVVEAS EDFLPLLLLT ADRPPELQGV GANQAINQIN
HFGSFVRFFF NLPPPTDLIP VRMVLTTVDS ALHWATGSAC GPVHLNCPFR DPLDGSPTNW
SSNCLNGLDM WMSNAEPFTK YFQVQSHKSD GVTTGQITEI LQVIKEAKKG LLLIGAIHTE
DEIWASLLLA KELMWPVVAD VLSGVRLRKL FKPFVEKLTH VFVDHLDHAL FSDSVRNLIE
FDVVIQVGSR ITSKRVSQML EKCFPFAYIL VDKHPCRHDP SHLVTHRVQS NIVQFANCVL
KSRFPWRRSK LHGHLQALDG AIAREMSFQI SAESSLTEPY VAHMLSKALT SKSALFIGNS
MPIRDVDMYG CSSENSSHVV DMMLSAELPC QWIQVTGNRG ASGIDGLLSS ATGFAVGCKK
RVVCVVGDIS FLHDTNGLAI LKQRIARKPM TILVINNRGG GIFRLLPIAK KTEPSVLNQY
FYTAHDISIE NLCLAHGVRY VHVGTKSELE DALFVPSVEE MDCIVEVESS INANAIVHST
LERFARQAAE NSLGIVSASS FLHPMIKNVL LCQVSGIQYS QYRVKLCDRP TICSDEFSQF
HREGFILSLT LEDGSIGYGE VAPLNSNVEN LMDVEGQLQL VLHLMNEAKF SYMLPLLNGS
ISSWIWSELG ITASSIFPSV RCGLEMALLN AMAVRHDSSL LGILHYQKEE NGSAQPHSVQ
ICALLDSEGT PLEVAYVARK LVQEGFSAIK LKVGRRVSSV QDALVMQEVR RAVGVQIELR
ADANCRWTFE EAREFGLLVN SCNLKYIEEP VQNKDDLIRF HEETGLPVAL DETLDDFEEC
PLRMLTKYTH PGIVAVVIKP SVVGGFENAA LIARWAQQHG KMAVISAAYE SGLGLSAYIL
FASYLEMENV KASTEQKQGT PPSVAHGLGT YRWLSEDVMM NTLGIFRSPY SGFVEGFIAD
ASRNLKDVKI NNDVIVRTSK GIPVRRYELR VDVDGFSHFI RVHDVGENAE GSVALFLHGF
LGTGEEWIPI MTGISGSARC ISVDIPGHGR SRVQSHASET QTSPTFSMEM IAEALYKLIE
QITPGKVTIV GYSMGARIAL YMALRFSNKI EGAVVVSGSP GLKDPVARKI RSATDDSKAR
MMVDNGLYIF IENWYNGGLW KSLRNHPHFS KIAASRLLHG DVPSVAKLLS DLSSGRQPSL
WEELEDCDTN ISLVFGEKDV KYKQIATRMY REMSKSKKSV NNIIEIVEIP EAGHAVHLES
PLRVILALRK FLTRVHNSST ETELSQKLLL ALKEM
