XMT1_COFCA
ID XMT1_COFCA Reviewed; 372 AA.
AC A4GE69; A0A096VHX9; E5Q8J7; Q8RVL9;
DT 31-MAY-2011, integrated into UniProtKB/Swiss-Prot.
DT 11-DEC-2019, sequence version 2.
DT 03-AUG-2022, entry version 53.
DE RecName: Full=7-methylxanthosine synthase 1 {ECO:0000305};
DE EC=2.1.1.158 {ECO:0000303|PubMed:17434991};
DE AltName: Full=Xanthosine methyltransferase 1 {ECO:0000303|PubMed:17401201};
DE Short=CcXMT1 {ECO:0000303|PubMed:25249475};
DE Short=XMT {ECO:0000303|PubMed:17401201};
GN Name=XMT1 {ECO:0000303|PubMed:17401201, ECO:0000303|PubMed:25249475};
GN ORFNames=GSCOC_T00036338001 {ECO:0000312|EMBL:CDP12638.1};
OS Coffea canephora (Robusta coffee).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Gardenieae complex;
OC Bertiereae - Coffeeae clade; Coffeeae; Coffea.
OX NCBI_TaxID=49390;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND CRYSTALLIZATION.
RX PubMed=17401201; DOI=10.1107/s1744309107009268;
RA McCarthy A.A., Biget L., Lin C., Petiard V., Tanksley S.D., McCarthy J.G.;
RT "Cloning, expression, crystallization and preliminary X-ray analysis of the
RT XMT and DXMT N-methyltransferases from Coffea canephora (robusta).";
RL Acta Crystallogr. F 63:304-307(2007).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Leaf;
RX PubMed=12861362; DOI=10.1007/s00122-003-1310-4;
RA Campa C., Noirot M., Bourgeois M., Pervent M., Ky C.L., Chrestin H.,
RA Hamon S., de Kochko A.;
RT "Genetic mapping of a caffeoyl-coenzyme A 3-O-methyltransferase gene in
RT coffee trees. Impact on chlorogenic acid content.";
RL Theor. Appl. Genet. 107:751-756(2003).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=23376454; DOI=10.1016/j.gene.2013.01.035;
RA Mohanan S., Gowda K., Kandukuri S.V., Chandrashekar A.;
RT "Involvement of a novel intronic microRNA in cross regulation of N-
RT methyltransferase genes involved in caffeine biosynthesis in Coffea
RT canephora.";
RL Gene 519:107-112(2013).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], TISSUE SPECIFICITY, DEVELOPMENTAL
RP STAGE, GENE FAMILY, AND NOMENCLATURE.
RC STRAIN=cv. DH200-94;
RX PubMed=25249475; DOI=10.1007/s00425-014-2170-7;
RA Perrois C., Strickler S.R., Mathieu G., Lepelley M., Bedon L., Michaux S.,
RA Husson J., Mueller L., Privat I.;
RT "Differential regulation of caffeine metabolism in Coffea arabica (Arabica)
RT and Coffea canephora (Robusta).";
RL Planta 241:179-191(2015).
RN [5]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Leaf;
RA Kretschmar J.A., Baumann T.W.;
RT "N-methyltransferases in the genus Coffea.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], TISSUE SPECIFICITY, AND
RP DEVELOPMENTAL STAGE.
RC STRAIN=cv. DH200-94;
RX PubMed=25190796; DOI=10.1126/science.1255274;
RA Denoeud F., Carretero-Paulet L., Dereeper A., Droc G., Guyot R.,
RA Pietrella M., Zheng C., Alberti A., Anthony F., Aprea G., Aury J.M.,
RA Bento P., Bernard M., Bocs S., Campa C., Cenci A., Combes M.C.,
RA Crouzillat D., Da Silva C., Daddiego L., De Bellis F., Dussert S.,
RA Garsmeur O., Gayraud T., Guignon V., Jahn K., Jamilloux V., Joet T.,
RA Labadie K., Lan T., Leclercq J., Lepelley M., Leroy T., Li L.T.,
RA Librado P., Lopez L., Munoz A., Noel B., Pallavicini A., Perrotta G.,
RA Poncet V., Pot D., Priyono X., Rigoreau M., Rouard M., Rozas J.,
RA Tranchant-Dubreuil C., VanBuren R., Zhang Q., Andrade A.C., Argout X.,
RA Bertrand B., de Kochko A., Graziosi G., Henry R.J., Jayarama X., Ming R.,
RA Nagai C., Rounsley S., Sankoff D., Giuliano G., Albert V.A., Wincker P.,
RA Lashermes P.;
RT "The coffee genome provides insight into the convergent evolution of
RT caffeine biosynthesis.";
RL Science 345:1181-1184(2014).
RN [7]
RP REVIEW ON CAFFEINE BIOSYNTHESIS.
RX PubMed=18068204; DOI=10.1016/j.phytochem.2007.10.029;
RA Ashihara H., Sano H., Crozier A.;
RT "Caffeine and related purine alkaloids: biosynthesis, catabolism, function
RT and genetic engineering.";
RL Phytochemistry 69:841-856(2008).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-HOMOCYSTEINE AND XANTHOSINE, FUNCTION, SUBUNIT, CATALYTIC
RP ACTIVITY, AND PATHWAY.
RX PubMed=17434991; DOI=10.1104/pp.106.094854;
RA McCarthy A.A., McCarthy J.G.;
RT "The structure of two N-methyltransferases from the caffeine biosynthetic
RT pathway.";
RL Plant Physiol. 144:879-889(2007).
CC -!- FUNCTION: Involved in the biosynthesis of caffeine (PubMed:17401201,
CC PubMed:17434991). Specific for xanthosine (PubMed:17434991). Cannot use
CC xanthosine 5'-monophosphate (XMP) as substrate (PubMed:17434991).
CC Directly produces 7-methylxanthine, and therefore the methyl transfer
CC and nucleoside cleavage may be coupled (PubMed:17434991). Catalyzes the
CC 7-N-methylation of xanthosine, but does not have 1-N- or 3-N-
CC methylation activity (PubMed:17434991). {ECO:0000269|PubMed:17401201,
CC ECO:0000269|PubMed:17434991}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-adenosyl-L-methionine + xanthosine = 7-methylxanthosine + S-
CC adenosyl-L-homocysteine; Xref=Rhea:RHEA:15025, ChEBI:CHEBI:18107,
CC ChEBI:CHEBI:49310, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789;
CC EC=2.1.1.158; Evidence={ECO:0000269|PubMed:17434991};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:15026;
CC Evidence={ECO:0000269|PubMed:17434991};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q9FLN8};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000250|UniProtKB:Q9FLN8};
CC -!- PATHWAY: Alkaloid biosynthesis. {ECO:0000269|PubMed:17434991}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:17434991}.
CC -!- TISSUE SPECIFICITY: Mainly expressed in leaves and fruits (grains)
CC (PubMed:25249475, PubMed:25190796). Also present, at lower levels, in
CC roots, stamens and pistils (PubMed:25190796).
CC {ECO:0000269|PubMed:25190796, ECO:0000269|PubMed:25249475}.
CC -!- DEVELOPMENTAL STAGE: In leaves, mostly expressed in young tissues
CC (PubMed:25249475). In fruits, highly expressed in green grains but
CC fades out as they are yellowing to disappear in red mature grains
CC (PubMed:25249475, PubMed:25190796). {ECO:0000269|PubMed:25190796,
CC ECO:0000269|PubMed:25249475}.
CC -!- SIMILARITY: Belongs to the methyltransferase superfamily. Type-7
CC methyltransferase family. {ECO:0000305}.
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DR EMBL; DQ422954; ABD90685.1; -; mRNA.
DR EMBL; AY273813; AAQ16154.1; -; mRNA.
DR EMBL; HQ616706; ADR30038.1; -; mRNA.
DR EMBL; JX978509; AFV60437.1; -; Genomic_DNA.
DR EMBL; JX978518; AFV60446.1; -; mRNA.
DR EMBL; AF494416; AAM18506.1; -; mRNA.
DR EMBL; HG739152; CDP12638.1; -; Genomic_DNA.
DR PDB; 2EG5; X-ray; 2.20 A; A/C/E/G=1-372.
DR PDBsum; 2EG5; -.
DR AlphaFoldDB; A4GE69; -.
DR SMR; A4GE69; -.
DR EnsemblPlants; CDP12638; CDP12638; GSCOC_T00036338001.
DR Gramene; CDP12638; CDP12638; GSCOC_T00036338001.
DR KEGG; ag:ABD90685; -.
DR OMA; TFQIYLN; -.
DR BRENDA; 2.1.1.158; 7042.
DR EvolutionaryTrace; A4GE69; -.
DR Proteomes; UP000295252; Chromosome 9.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0009820; P:alkaloid metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR Gene3D; 1.10.1200.270; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR005299; MeTrfase_7.
DR InterPro; IPR042086; MeTrfase_capping.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR31009; PTHR31009; 1.
DR Pfam; PF03492; Methyltransf_7; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alkaloid metabolism; Magnesium; Metal-binding;
KW Methyltransferase; Reference proteome; S-adenosyl-L-methionine;
KW Transferase.
FT CHAIN 1..372
FT /note="7-methylxanthosine synthase 1"
FT /id="PRO_0000408469"
FT BINDING 18
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:A4GE70"
FT BINDING 18
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:A4GE70"
FT BINDING 21..25
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17434991,
FT ECO:0007744|PDB:2EG5"
FT BINDING 61..62
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q9FLN8"
FT BINDING 61
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:17434991,
FT ECO:0007744|PDB:2EG5"
FT BINDING 62
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:A0A6C0WW36"
FT BINDING 67
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:A4GE70"
FT BINDING 99..102
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:17434991,
FT ECO:0007744|PDB:2EG5"
FT BINDING 140..142
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:17434991,
FT ECO:0007744|PDB:2EG5"
FT BINDING 157..159
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:17434991,
FT ECO:0007744|PDB:2EG5"
FT BINDING 158..162
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17434991,
FT ECO:0007744|PDB:2EG5"
FT BINDING 179
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q9FLN8"
FT BINDING 261
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q9FLN8"
FT BINDING 263
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q9FLN8"
FT BINDING 264
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q9FLN8"
FT BINDING 316
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17434991,
FT ECO:0007744|PDB:2EG5"
FT BINDING 321
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17434991,
FT ECO:0007744|PDB:2EG5"
FT BINDING 356
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17434991,
FT ECO:0007744|PDB:2EG5"
FT SITE 155
FT /note="Involved in substrate discrimination"
FT /evidence="ECO:0000250|UniProtKB:Q9FZN8"
FT SITE 267
FT /note="Involved in substrate discrimination"
FT /evidence="ECO:0000250|UniProtKB:Q9FZN8"
FT SITE 331
FT /note="Involved in substrate discrimination"
FT /evidence="ECO:0000250|UniProtKB:Q9FZN8"
FT CONFLICT 8
FT /note="R -> Q (in Ref. 4; AFV60437/AFV60446)"
FT /evidence="ECO:0000305"
FT CONFLICT 174..177
FT /note="SGIS -> LGIG (in Ref. 1; ABD90685)"
FT /evidence="ECO:0000305"
FT CONFLICT 174
FT /note="S -> L (in Ref. 3; ADR30038)"
FT /evidence="ECO:0000305"
FT CONFLICT 372
FT /note="V -> M (in Ref. 1; ABD90685)"
FT /evidence="ECO:0000305"
FT STRAND 16..18
FT /evidence="ECO:0007829|PDB:2EG5"
FT HELIX 25..45
FT /evidence="ECO:0007829|PDB:2EG5"
FT TURN 49..53
FT /evidence="ECO:0007829|PDB:2EG5"
FT STRAND 54..61
FT /evidence="ECO:0007829|PDB:2EG5"
FT HELIX 66..82
FT /evidence="ECO:0007829|PDB:2EG5"
FT STRAND 94..100
FT /evidence="ECO:0007829|PDB:2EG5"
FT HELIX 107..112
FT /evidence="ECO:0007829|PDB:2EG5"
FT HELIX 114..125
FT /evidence="ECO:0007829|PDB:2EG5"
FT STRAND 131..136
FT /evidence="ECO:0007829|PDB:2EG5"
FT STRAND 151..158
FT /evidence="ECO:0007829|PDB:2EG5"
FT STRAND 164..166
FT /evidence="ECO:0007829|PDB:2EG5"
FT TURN 168..172
FT /evidence="ECO:0007829|PDB:2EG5"
FT HELIX 191..215
FT /evidence="ECO:0007829|PDB:2EG5"
FT STRAND 216..228
FT /evidence="ECO:0007829|PDB:2EG5"
FT HELIX 238..251
FT /evidence="ECO:0007829|PDB:2EG5"
FT STRAND 253..255
FT /evidence="ECO:0007829|PDB:2EG5"
FT TURN 259..262
FT /evidence="ECO:0007829|PDB:2EG5"
FT HELIX 272..282
FT /evidence="ECO:0007829|PDB:2EG5"
FT STRAND 284..296
FT /evidence="ECO:0007829|PDB:2EG5"
FT TURN 297..300
FT /evidence="ECO:0007829|PDB:2EG5"
FT HELIX 309..329
FT /evidence="ECO:0007829|PDB:2EG5"
FT HELIX 331..333
FT /evidence="ECO:0007829|PDB:2EG5"
FT HELIX 334..348
FT /evidence="ECO:0007829|PDB:2EG5"
FT HELIX 349..351
FT /evidence="ECO:0007829|PDB:2EG5"
FT STRAND 354..365
FT /evidence="ECO:0007829|PDB:2EG5"
SQ SEQUENCE 372 AA; 41816 MW; D1449F54552081F3 CRC64;
MELQEVLRMN GGEGDTSYAK NSAYNQLVLA KVKPVLEQCV RELLRANLPN INKCIKVADL
GCASGPNTLL TVRDIVQSID KVGQEKKNEL ERPTIQIFLN DLFPNDFNSV FKLLPSFYRK
LEKENGRKIG SCLIGAMPGS FYSRLFPEES MHFLHSCYCL QWLSQVPSGL VTESGISTNK
GSIYSSKASR LPVQKAYLDQ FTKDFTTFLR IHSEELFSHG RMLLTCICKG VELDARNAID
LLEMAINDLV VEGHLEEEKL DSFNLPVYIP SAEEVKCIVE EEGSFEILYL ETFKVLYDAG
FSIDDEHIKA EYVASSVRAV YEPILASHFG EAIIPDIFHR FAKHAAKVLP LGKGFYNNLI
ISLAKKPEKS DV
