RBCMT_PEA
ID RBCMT_PEA Reviewed; 489 AA.
AC Q43088;
DT 24-OCT-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic;
DE EC=2.1.1.127;
DE AltName: Full=[Fructose-bisphosphate aldolase]-lysine N-methyltransferase;
DE EC=2.1.1.259;
DE AltName: Full=[Ribulose-bisphosphate carboxylase]-lysine N-methyltransferase;
DE Short=PsLSMT;
DE Short=RuBisCO LSMT;
DE Short=RuBisCO methyltransferase;
DE Short=rbcMT;
DE Flags: Precursor;
GN Name=RBCMT;
OS Pisum sativum (Garden pea).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; Hologalegina; IRL clade; Fabeae; Pisum.
OX NCBI_TaxID=3888;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND PARTIAL PROTEIN SEQUENCE.
RC TISSUE=Leaf;
RX PubMed=7888616; DOI=10.1007/bf00020181;
RA Klein R.R., Houtz R.L.;
RT "Cloning and developmental expression of pea ribulose-1,5-bisphosphate
RT carboxylase/oxygenase large subunit N-methyltransferase.";
RL Plant Mol. Biol. 27:249-261(1995).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 46-482 IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE, CATALYTIC ACTIVITY, SUBUNIT, MUTAGENESIS OF
RP GLU-281, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=12372303; DOI=10.1016/s0092-8674(02)01000-0;
RA Trievel R.C., Beach B.M., Dirk L.M., Houtz R.L., Hurley J.H.;
RT "Structure and catalytic mechanism of a SET domain protein
RT methyltransferase.";
RL Cell 111:91-103(2002).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.55 ANGSTROMS) OF 46-482 IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE AND SUBSTRATE.
RX PubMed=12819771; DOI=10.1038/nsb946;
RA Trievel R.C., Flynn E.M., Houtz R.L., Hurley J.H.;
RT "Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco
RT LSMT.";
RL Nat. Struct. Biol. 10:545-552(2003).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) OF 49-482 IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE AND SUBSTRATE.
RX PubMed=16682405; DOI=10.1074/jbc.m602257200;
RA Couture J.F., Hauk G., Thompson M.J., Blackburn G.M., Trievel R.C.;
RT "Catalytic roles for carbon-oxygen hydrogen bonding in SET domain lysine
RT methyltransferases.";
RL J. Biol. Chem. 281:19280-19287(2006).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=22547063; DOI=10.1074/jbc.m112.359976;
RA Mininno M., Brugiere S., Pautre V., Gilgen A., Ma S., Ferro M., Tardif M.,
RA Alban C., Ravanel S.;
RT "Characterization of chloroplastic fructose 1,6-bisphosphate aldolases as
RT lysine-methylated proteins in plants.";
RL J. Biol. Chem. 287:21034-21044(2012).
CC -!- FUNCTION: Methylates 'Lys-14' of the large subunit of RuBisCO. Can also
CC use with lower efficiency chloroplastic fructose-bisphosphate aldolases
CC and gamma-tocopherol methyltransferase as substrates, but not a
CC cytosolic aldolase. {ECO:0000269|PubMed:22547063}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysyl-[ribulose-1,5-bisphosphate carboxylase] + 3 S-
CC adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-
CC [ribulose-1,5-bisphosphate carboxylase] + 3 S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:50996, Rhea:RHEA-COMP:12858, Rhea:RHEA-
CC COMP:12859, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.127;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[fructose-bisphosphate aldolase]-L-lysine + 3 S-adenosyl-L-
CC methionine = [fructose-bisphosphate aldolase]-N(6),N(6),N(6)-
CC trimethyl-L-lysine + 3 H(+) + 3 S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:51000, Rhea:RHEA-COMP:12861, Rhea:RHEA-COMP:12862,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.259;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=12.9 uM for fructose-bisphosphate aldolase 2
CC {ECO:0000269|PubMed:12372303, ECO:0000269|PubMed:22547063};
CC KM=14.0 uM for fructose-bisphosphate aldolase 3
CC {ECO:0000269|PubMed:12372303, ECO:0000269|PubMed:22547063};
CC KM=32.0 uM for gamma-tocopherol methyltransferase
CC {ECO:0000269|PubMed:12372303, ECO:0000269|PubMed:22547063};
CC KM=4.5 uM for rubisco {ECO:0000269|PubMed:12372303,
CC ECO:0000269|PubMed:22547063};
CC KM=6 uM for S-adenosyl-L-methionine {ECO:0000269|PubMed:12372303,
CC ECO:0000269|PubMed:22547063};
CC Vmax=19.5 nmol/min/mg enzyme with fructose-bisphosphate aldolase 2 as
CC substrate {ECO:0000269|PubMed:12372303, ECO:0000269|PubMed:22547063};
CC Vmax=9.0 nmol/min/mg enzyme with fructose-bisphosphate aldolase 3 as
CC substrate {ECO:0000269|PubMed:12372303, ECO:0000269|PubMed:22547063};
CC Vmax=1.7 nmol/min/mg enzyme with gamma-tocopherol methyltransferase
CC as substrate {ECO:0000269|PubMed:12372303,
CC ECO:0000269|PubMed:22547063};
CC Vmax=44.6 nmol/min/mg enzyme with rubisco as substrate
CC {ECO:0000269|PubMed:12372303, ECO:0000269|PubMed:22547063};
CC Vmax=56 nmol/min/mg enzyme with S-adenosyl-L-methionine as substrate
CC {ECO:0000269|PubMed:12372303, ECO:0000269|PubMed:22547063};
CC Note=kcat is 0.047 sec(-1) for S-adenosyl-L-methionine. kcat is 0.038
CC sec(-1) for rubisco.;
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:12372303,
CC ECO:0000269|PubMed:12819771, ECO:0000269|PubMed:16682405}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast.
CC -!- TISSUE SPECIFICITY: Highly expressed in leaf.
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. Plant protein-lysine LSMT methyltransferase family.
CC {ECO:0000255|PROSITE-ProRule:PRU00916}.
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DR EMBL; L34291; AAA69903.1; -; mRNA.
DR PIR; S53005; S53005.
DR PDB; 1MLV; X-ray; 2.60 A; A/B/C=46-482.
DR PDB; 1OZV; X-ray; 2.65 A; A/B/C=46-482.
DR PDB; 1P0Y; X-ray; 2.55 A; A/B/C=46-482.
DR PDB; 2H21; X-ray; 2.45 A; A/B/C=49-482.
DR PDB; 2H23; X-ray; 2.45 A; A/B/C=49-482.
DR PDB; 2H2E; X-ray; 2.60 A; A/B/C=49-482.
DR PDB; 2H2J; X-ray; 2.45 A; A/B/C=49-482.
DR PDBsum; 1MLV; -.
DR PDBsum; 1OZV; -.
DR PDBsum; 1P0Y; -.
DR PDBsum; 2H21; -.
DR PDBsum; 2H23; -.
DR PDBsum; 2H2E; -.
DR PDBsum; 2H2J; -.
DR AlphaFoldDB; Q43088; -.
DR SMR; Q43088; -.
DR DIP; DIP-48722N; -.
DR IntAct; Q43088; 3.
DR EnsemblPlants; Psat7g156240.1; Psat7g156240.1.cds1; Psat7g156240.
DR Gramene; Psat7g156240.1; Psat7g156240.1.cds1; Psat7g156240.
DR KEGG; ag:AAA69903; -.
DR BRENDA; 2.1.1.127; 4872.
DR BRENDA; 2.1.1.259; 4872.
DR SABIO-RK; Q43088; -.
DR EvolutionaryTrace; Q43088; -.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0030785; F:[ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0016279; F:protein-lysine N-methyltransferase activity; IEA:InterPro.
DR GO; GO:0018022; P:peptidyl-lysine methylation; IEA:InterPro.
DR CDD; cd19179; SET_RBCMT; 1.
DR Gene3D; 3.90.1420.10; -; 1.
DR InterPro; IPR011192; Rubisco_LSMT_MeTrfase_plant.
DR InterPro; IPR015353; Rubisco_LSMT_subst-bd.
DR InterPro; IPR036464; Rubisco_LSMT_subst-bd_sf.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR InterPro; IPR044431; SET_RBCMT.
DR Pfam; PF09273; Rubis-subs-bind; 1.
DR Pfam; PF00856; SET; 1.
DR PIRSF; PIRSF009328; RMT_SET; 1.
DR SMART; SM00317; SET; 1.
DR SUPFAM; SSF81822; SSF81822; 1.
DR SUPFAM; SSF82199; SSF82199; 1.
DR PROSITE; PS51583; SAM_MT127; 1.
DR PROSITE; PS50280; SET; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chloroplast; Direct protein sequencing; Methyltransferase;
KW Plastid; S-adenosyl-L-methionine; Transferase; Transit peptide.
FT TRANSIT 1..37
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 38..489
FT /note="Ribulose-1,5 bisphosphate carboxylase/oxygenase
FT large subunit N-methyltransferase, chloroplastic"
FT /id="PRO_0000022199"
FT DOMAIN 64..288
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 80..82
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 222
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190,
FT ECO:0000269|PubMed:12372303, ECO:0000269|PubMed:12819771,
FT ECO:0000269|PubMed:16682405"
FT BINDING 222
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:12819771,
FT ECO:0000269|PubMed:16682405"
FT BINDING 226
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:12819771,
FT ECO:0000269|PubMed:16682405"
FT BINDING 239
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:12819771,
FT ECO:0000269|PubMed:16682405"
FT BINDING 242..243
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 254
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:12819771,
FT ECO:0000269|PubMed:16682405"
FT BINDING 287
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:12819771,
FT ECO:0000269|PubMed:16682405"
FT BINDING 300
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:12819771,
FT ECO:0000269|PubMed:16682405"
FT MUTAGEN 281
FT /note="E->Q: No effect on substrate affinity, but reduced
FT catalytic activity."
FT /evidence="ECO:0000269|PubMed:12372303"
FT HELIX 52..63
FT /evidence="ECO:0007829|PDB:2H21"
FT STRAND 66..70
FT /evidence="ECO:0007829|PDB:2H2E"
FT STRAND 72..78
FT /evidence="ECO:0007829|PDB:2H21"
FT STRAND 81..88
FT /evidence="ECO:0007829|PDB:2H21"
FT STRAND 94..100
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 101..103
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 107..110
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 116..119
FT /evidence="ECO:0007829|PDB:2H21"
FT STRAND 120..122
FT /evidence="ECO:0007829|PDB:1P0Y"
FT HELIX 124..137
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 144..147
FT /evidence="ECO:0007829|PDB:2H21"
FT TURN 157..159
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 162..166
FT /evidence="ECO:0007829|PDB:2H21"
FT TURN 167..170
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 172..194
FT /evidence="ECO:0007829|PDB:2H21"
FT TURN 198..202
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 209..222
FT /evidence="ECO:0007829|PDB:2H21"
FT STRAND 226..229
FT /evidence="ECO:0007829|PDB:1P0Y"
FT STRAND 231..233
FT /evidence="ECO:0007829|PDB:1P0Y"
FT HELIX 238..240
FT /evidence="ECO:0007829|PDB:2H2J"
FT STRAND 253..255
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 258..260
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 264..266
FT /evidence="ECO:0007829|PDB:2H21"
FT STRAND 268..275
FT /evidence="ECO:0007829|PDB:2H21"
FT STRAND 281..285
FT /evidence="ECO:0007829|PDB:2H23"
FT HELIX 293..299
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 307..309
FT /evidence="ECO:0007829|PDB:2H21"
FT STRAND 311..317
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 325..333
FT /evidence="ECO:0007829|PDB:2H21"
FT TURN 334..336
FT /evidence="ECO:0007829|PDB:2H21"
FT STRAND 339..346
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 355..363
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 366..372
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 374..376
FT /evidence="ECO:0007829|PDB:2H21"
FT TURN 377..379
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 380..386
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 390..408
FT /evidence="ECO:0007829|PDB:2H21"
FT STRAND 411..413
FT /evidence="ECO:0007829|PDB:1P0Y"
FT HELIX 415..422
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 428..456
FT /evidence="ECO:0007829|PDB:2H21"
FT TURN 457..460
FT /evidence="ECO:0007829|PDB:2H21"
FT HELIX 464..469
FT /evidence="ECO:0007829|PDB:2H21"
FT STRAND 474..476
FT /evidence="ECO:0007829|PDB:2H2E"
FT HELIX 479..482
FT /evidence="ECO:0007829|PDB:2H21"
SQ SEQUENCE 489 AA; 55110 MW; 72C53E37EE08AFC5 CRC64;
MATIFSGGSV SPFLFHTNKG TSFTPKAPIL HLKRSFSAKS VASVGTEPSL SPAVQTFWKW
LQEEGVITAK TPVKASVVTE GLGLVALKDI SRNDVILQVP KRLWINPDAV AASEIGRVCS
ELKPWLSVIL FLIRERSRED SVWKHYFGIL PQETDSTIYW SEEELQELQG SQLLKTTVSV
KEYVKNECLK LEQEIILPNK RLFPDPVTLD DFFWAFGILR SRAFSRLRNE NLVVVPMADL
INHSAGVTTE DHAYEVKGAA GLFSWDYLFS LKSPLSVKAG EQVYIQYDLN KSNAELALDY
GFIEPNENRH AYTLTLEISE SDPFFDDKLD VAESNGFAQT AYFDIFYNRT LPPGLLPYLR
LVALGGTDAF LLESLFRDTI WGHLELSVSR DNEELLCKAV REACKSALAG YHTTIEQDRE
LKEGNLDSRL AIAVGIREGE KMVLQQIDGI FEQKELELDQ LEYYQERRLK DLGLCGENGD
ILGDLGKFF
