1MLV

Structure and Catalytic Mechanism of a SET Domain Protein Methyltransferase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1mlva1	All alpha proteins	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	pea (Pisum sativum ) [TaxId: 3888 ],	SCOPe (2.08)
A	d1mlva2	All beta proteins	beta-clip	SET domain	RuBisCo LSMT catalytic domain	RuBisCo LSMT catalytic domain	pea (Pisum sativum ) [TaxId: 3888 ],	SCOPe (2.08)
A	d1mlva3	Artifacts	Tags	Tags	Tags	C-terminal Tags	pea (Pisum sativum ) [TaxId: 3888 ],	SCOPe (2.08)
B	d1mlvb1	All alpha proteins	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	pea (Pisum sativum ) [TaxId: 3888 ],	SCOPe (2.08)
B	d1mlvb2	All beta proteins	beta-clip	SET domain	RuBisCo LSMT catalytic domain	RuBisCo LSMT catalytic domain	pea (Pisum sativum ) [TaxId: 3888 ],	SCOPe (2.08)
B	d1mlvb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	pea (Pisum sativum ) [TaxId: 3888 ],	SCOPe (2.08)
C	d1mlvc1	All alpha proteins	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	RuBisCo LSMT C-terminal, substrate-binding domain	pea (Pisum sativum ) [TaxId: 3888 ],	SCOPe (2.08)
C	d1mlvc2	All beta proteins	beta-clip	SET domain	RuBisCo LSMT catalytic domain	RuBisCo LSMT catalytic domain	pea (Pisum sativum ) [TaxId: 3888 ],	SCOPe (2.08)
C	d1mlvc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	pea (Pisum sativum ) [TaxId: 3888 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SET domain	8042118	3000162	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RuBisCo LSMT C-terminal, substrate-binding domain	8042117	3001192	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SET domain	8042118	3000162	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RuBisCo LSMT C-terminal, substrate-binding domain	8042117	3001192	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SET domain	8042118	3000162	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RuBisCo LSMT C-terminal, substrate-binding domain	8042117	3001192	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SET_5	e1mlvA1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET_5	ECOD (1.6)
A	Rubis-subs-bind	e1mlvA2	A: a+b complex topology	X: RuBisCo LSMT C-terminal, substrate-binding domain (From Topology)	H: RuBisCo LSMT C-terminal, substrate-binding domain (From Topology)	T: RuBisCo LSMT C-terminal, substrate-binding domain	F: Rubis-subs-bind	ECOD (1.6)
B	SET_5	e1mlvB1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET_5	ECOD (1.6)
B	Rubis-subs-bind	e1mlvB2	A: a+b complex topology	X: RuBisCo LSMT C-terminal, substrate-binding domain (From Topology)	H: RuBisCo LSMT C-terminal, substrate-binding domain (From Topology)	T: RuBisCo LSMT C-terminal, substrate-binding domain	F: Rubis-subs-bind	ECOD (1.6)
C	SET_5	e1mlvC1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET_5	ECOD (1.6)
C	Rubis-subs-bind	e1mlvC2	A: a+b complex topology	X: RuBisCo LSMT C-terminal, substrate-binding domain (From Topology)	H: RuBisCo LSMT C-terminal, substrate-binding domain (From Topology)	T: RuBisCo LSMT C-terminal, substrate-binding domain	F: Rubis-subs-bind	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.1410.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 1	set domain protein methyltransferase, domain 1	CATH (4.3.0)
A	3.90.1420.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 2	Rubisco LSMT, substrate-binding domain	CATH (4.3.0)
B	3.90.1410.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 1	set domain protein methyltransferase, domain 1	CATH (4.3.0)
B	3.90.1420.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 2	Rubisco LSMT, substrate-binding domain	CATH (4.3.0)
C	3.90.1410.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 1	set domain protein methyltransferase, domain 1	CATH (4.3.0)
C	3.90.1420.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 2	Rubisco LSMT, substrate-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF09273	Rubisco LSMT substrate-binding (Rubis-subs-bind)	Rubisco LSMT substrate-binding	Members of this family adopt a multihelical structure, with an irregular array of long and short alpha-helices. They allow binding of the protein to substrate, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco ho ...	Members of this family adopt a multihelical structure, with an irregular array of long and short alpha-helices. They allow binding of the protein to substrate, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase	protein-lysine N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups lysine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity	methylation metabolic process cellular process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR050600	SETD3/SETD6 methyltransferase	Family
A, B, C	IPR036464	Rubisco LSMT, substrate-binding domain superfamily	Homologous Superfamily
A, B, C	IPR046341	SET domain superfamily	Homologous Superfamily
A, B, C	IPR011192	Rubisco LSMT methyltransferase, plant	Family
A, B, C	IPR015353	Rubisco LSMT, substrate-binding domain	Domain
A, B, C	IPR001214	SET domain	Domain
A, B, C	IPR044431	RBCMT, SET domain	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	[ribulose-bisphosphate carboxylase]-lysine N-methyltransferase M-CSA #604	Ribulose-1,5-bisphosphate carboxylase-oxygenase large subunit N-methyltransferase enzymes (LSMTs) uses S-adenosyl methionine to methylate Lys 14 of the Rubisco large subunit. Lys 14 is situated in the flexible N-terminal tail of the large subunit, and the precise role of its methylation is not clear. It does not affect the activity of Rubisco but may be involved in targeting other proteins to interact with the tail.	Defined by 1 residue: TYR:A-243 [auth A-287] \| Explore in 3D: M-CSA Motif Definition At least 2 residues must be present to support Structure Motif searching. EC: 2.1.1.127 (PDB Primary Data) EC: 2.1.1.259 (UniProt)

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.