1P0Y

Crystal structure of the SET domain of LSMT bound to MeLysine and AdoHcy

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1p0ya1	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	d1p0ya2	All beta proteins	beta-clip	SET domain	RuBisCo LSMT catalytic domain	RuBisCo LSMT catalytic domain	pea (Pisum sativum ) [TaxId: 3888 ],	SCOPe (2.08)
A	d1p0ya3	Artifacts	Tags	Tags	Tags	C-terminal Tags	pea (Pisum sativum ) [TaxId: 3888 ],	SCOPe (2.08)
B	d1p0yb1	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	d1p0yb2	All beta proteins	beta-clip	SET domain	RuBisCo LSMT catalytic domain	RuBisCo LSMT catalytic domain	pea (Pisum sativum ) [TaxId: 3888 ],	SCOPe (2.08)
B	d1p0yb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	pea (Pisum sativum ) [TaxId: 3888 ],	SCOPe (2.08)
C	d1p0yc1	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	d1p0yc2	All beta proteins	beta-clip	SET domain	RuBisCo LSMT catalytic domain	RuBisCo LSMT catalytic domain	pea (Pisum sativum ) [TaxId: 3888 ],	SCOPe (2.08)
C	d1p0yc3	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	RuBisCo LSMT C-terminal substrate-binding domain	8042117	3001192	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SET domain	8042118	3000162	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	e1p0yA1	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	e1p0yA2	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	e1p0yB1	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	e1p0yB2	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	e1p0yC1	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	e1p0yC2	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 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast	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	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.