Homocysteine S-methyltransferase superfamily

SCOP classification

• Root: SCOP hierarchy in SUPERFAMILY [ 0] (11)
• Class: Alpha and beta proteins (a/b) [ 51349] (147)
• Fold: TIM beta/alpha-barrel [ 51350] (33)
• Superfamily: Homocysteine S-methyltransferase [ 82282]
• Families: Homocysteine S-methyltransferase [ 82283] (2)

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Superfamily statistics

	Genomes (2,170)	Uniprot 2018_03 genome	PDB chains (SCOP 1.75)
Domains	3,579	26,879	3
Proteins	3,553	26,765	3

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Functional annotation

• General category: Metabolism
• Detailed category: Transferases

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Enzyme Commission (EC)

Highlighted in gray are those with FDR_all>0.001

	EC term	FDR (all)	IC level	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Betaine--homocysteine S-methyltransferase	0	2.56	--	DIRECT
Enzyme Commission (EC)	Homocysteine S-methyltransferase	0	2.56	--	DIRECT
Enzyme Commission (EC)	Transferases	0	0	--	DIRECT
Enzyme Commission (EC)	Transferring one-carbon groups	0	0.7211	Least Informative	DIRECT
Enzyme Commission (EC)	Methyltransferases	0	0.8609	Moderately Informative	DIRECT
Enzyme Commission (EC)	Methionine synthase	0	1.861	Highly Informative	DIRECT

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Disease Ontology (DO)

Highlighted in gray are those with FDR_all>0.001

	DO term	FDR (all)	IC level	SDDO level	Annotation (direct or inherited)
Disease Ontology (DO)	inherited metabolic disorder	0	1.292	--	DIRECT
Disease Ontology (DO)	amino acid metabolic disorder	0	2.371	--	DIRECT
Disease Ontology (DO)	hyperhomocysteinemia	0	2.371	--	DIRECT
Disease Ontology (DO)	disease of metabolism	0	1.029	Moderately Informative	DIRECT

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Xenopus Anatomy (XA)

Highlighted in gray are those with FDR_all>0.001

	XA term	FDR (all)	IC level	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	head region	0	0.5108	--	DIRECT
Xenopus ANatomical entity (XAN)	trunk region	0	0.4287	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical structure	0	0	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical group	0	0.1442	--	DIRECT
Xenopus ANatomical entity (XAN)	organism subdivision	0	0.1871	--	DIRECT
Xenopus ANatomical entity (XAN)	compound organ	0	0.24	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical region	0	0.193	--	DIRECT
Xenopus ANatomical entity (XAN)	multicellular anatomical structure	0	0.1217	--	DIRECT
Xenopus ANatomical entity (XAN)	whole organism	1	0.09747	--	INHERITED FROM: head region || anatomical group || cavitated compound organ || multicellular anatomical structure || compound organ || trunk || anatomical region || trunk region || organism subdivision || head
Xenopus ANatomical entity (XAN)	head	0	0.5108	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	trunk	0	0.4308	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	cavitated compound organ	0	0.3033	Least Informative	DIRECT
Xenopus DEvelopment stage (XDE)	NF stage	0	0.02327	--	DIRECT
Xenopus DEvelopment stage (XDE)	unspecified stage	0	1.131	Moderately Informative	DIRECT

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Arabidopsis Plant Ontology (AP)

Highlighted in gray are those with FDR_all>0.001

	AP term	FDR (all)	IC level	SDAP level	Annotation (direct or inherited)
Plant ANatomical entity (PAN)	stem internode	0	0.6495	--	DIRECT
Plant ANatomical entity (PAN)	phyllome apex	0	0.7019	--	DIRECT
Plant ANatomical entity (PAN)	stamen	0	0.6028	--	DIRECT
Plant ANatomical entity (PAN)	epidermal cell	0	0.2569	--	DIRECT
Plant ANatomical entity (PAN)	gynoecium	0	0.6058	--	DIRECT
Plant ANatomical entity (PAN)	sporophyll	0	0.4713	--	DIRECT
Plant ANatomical entity (PAN)	cauline leaf	0	0.7019	--	DIRECT
Plant ANatomical entity (PAN)	shoot system	0	0.05747	--	DIRECT
Plant ANatomical entity (PAN)	shoot epidermal cell	0	0.276	--	DIRECT
Plant ANatomical entity (PAN)	shoot epidermis	0	0.2691	--	DIRECT
Plant ANatomical entity (PAN)	stem	0	0.577	--	DIRECT
Plant ANatomical entity (PAN)	cardinal organ part	0	0.51	--	DIRECT
Plant ANatomical entity (PAN)	perianth	0	0.5448	--	DIRECT
Plant ANatomical entity (PAN)	shoot internode	0	0.6463	--	DIRECT
Plant ANatomical entity (PAN)	phyllome	0	0.3809	--	DIRECT
Plant ANatomical entity (PAN)	corolla	0	0.594	--	DIRECT
Plant ANatomical entity (PAN)	portion of plant tissue	0	0.1892	--	DIRECT
Plant ANatomical entity (PAN)	collective plant structure	0	0.01577	--	DIRECT
Plant ANatomical entity (PAN)	petal	0	0.594	--	DIRECT
Plant ANatomical entity (PAN)	calyx	0	0.5715	--	DIRECT
Plant ANatomical entity (PAN)	androecium	0	0.594	--	DIRECT
Plant ANatomical entity (PAN)	reproductive shoot system	0	0.4141	--	DIRECT
Plant ANatomical entity (PAN)	plant cell	0	0.1489	--	DIRECT
Plant ANatomical entity (PAN)	epidermis	0	0.2464	--	DIRECT
Plant ANatomical entity (PAN)	sepal	0	0.5715	--	DIRECT
Plant ANatomical entity (PAN)	stomatal complex	0	0.2774	--	DIRECT
Plant ANatomical entity (PAN)	collective leaf structure	0	0.55	--	DIRECT
Plant ANatomical entity (PAN)	shoot apex	0	0.5633	--	DIRECT
Plant ANatomical entity (PAN)	vascular leaf	0	0.5246	--	DIRECT
Plant ANatomical entity (PAN)	plant organ	0	0.2816	--	DIRECT
Plant ANatomical entity (PAN)	carpel	0	0.6087	--	DIRECT
Plant ANatomical entity (PAN)	plant axis	0	0.3881	--	DIRECT
Plant ANatomical entity (PAN)	leaf apex	0	0.7094	--	DIRECT
Plant ANatomical entity (PAN)	multi-tissue plant structure	0	0.2691	--	DIRECT
Plant ANatomical entity (PAN)	root	0	0.5579	--	DIRECT
Plant ANatomical entity (PAN)	collective plant organ structure	1	0.04502	--	INHERITED FROM: calyx || flower || sporophyll || root system || root || perianth || stem || leaf || phyllome || shoot internode || sepal || vascular leaf || gynoecium || petal || reproductive shoot system || shoot apex || leaf apex || carpel || collective phyllome structure || guard cell || megasporophyll || cauline leaf || microsporophyll || shoot epidermal cell || corolla || androecium || stomatal complex || phyllome apex || stamen || stem internode || shoot axis || shoot system || collective leaf structure || shoot epidermis
Plant ANatomical entity (PAN)	plant structure	1	0	--	INHERITED FROM: perianth || root || sporophyll || calyx || flower || collective plant structure || leaf || shoot internode || phyllome || cardinal organ part || multi-tissue plant structure || microsporophyll || guard cell || megasporophyll || cauline leaf || reproductive shoot system || shoot apex || leaf apex || collective leaf structure || stem internode || shoot system || portion of plant tissue || stomatal complex || plant organ || stem || whole plant || epidermis || root system || cardinal part of multi-tissue plant structure || gynoecium || vascular leaf || sepal || epidermal cell || shoot epidermal cell || corolla || plant axis || collective phyllome structure || petal || plant cell || carpel || shoot epidermis || phyllome apex || stamen || shoot axis || androecium
Plant ANatomical entity (PAN)	collective phyllome structure	0	0.4648	Least Informative	DIRECT
Plant ANatomical entity (PAN)	guard cell	0	0.2774	Least Informative	DIRECT
Plant ANatomical entity (PAN)	leaf	0	0.5053	Least Informative	DIRECT
Plant ANatomical entity (PAN)	megasporophyll	0	0.6087	Least Informative	DIRECT
Plant ANatomical entity (PAN)	shoot axis	0	0.4735	Least Informative	DIRECT
Plant ANatomical entity (PAN)	whole plant	0	0.4218	Least Informative	DIRECT
Plant ANatomical entity (PAN)	cardinal part of multi-tissue plant structure	0	0.5029	Least Informative	DIRECT
Plant ANatomical entity (PAN)	root system	0	0.5346	Least Informative	DIRECT
Plant ANatomical entity (PAN)	flower	0	0.4337	Least Informative	DIRECT
Plant ANatomical entity (PAN)	microsporophyll	0	0.5029	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	whole plant development stage	0	0.1968	--	DIRECT
Plant structure DEvelopment stage (PDE)	leaf production stage	0	0.3937	--	DIRECT
Plant structure DEvelopment stage (PDE)	1 main shoot growth stage	0	0.3937	--	DIRECT
Plant structure DEvelopment stage (PDE)	plant organ development stage	0	0.08108	--	DIRECT
Plant structure DEvelopment stage (PDE)	corolla development stage	0	0.1981	--	DIRECT
Plant structure DEvelopment stage (PDE)	flowering stage	0	0.2162	--	DIRECT
Plant structure DEvelopment stage (PDE)	collective plant organ structure development stage	0	0.03771	--	DIRECT
Plant structure DEvelopment stage (PDE)	floral organ formation stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	floral organ differentiation stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	reproductive shoot system development stage	0	0.05008	--	DIRECT
Plant structure DEvelopment stage (PDE)	sporophyte vegetative stage	0	0.2036	--	DIRECT
Plant structure DEvelopment stage (PDE)	collective phyllome structure development stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	phyllome development stage	0	0.4754	--	DIRECT
Plant structure DEvelopment stage (PDE)	life of whole plant stage	1	0.2022	--	INHERITED FROM: sporophyte vegetative stage || LP.10 ten leaves visible stage || LP.04 four leaves visible stage || LP.06 six leaves visible stage || LP.08 eight leaves visible stage || leaf production stage || 1 main shoot growth stage
Plant structure DEvelopment stage (PDE)	flower development stage	1	0.07083	--	INHERITED FROM: corolla development stage || flowering stage || floral organ differentiation stage || floral organ formation stage
Plant structure DEvelopment stage (PDE)	leaf development stage	1	0.4754	--	INHERITED FROM: 4 leaf senescence stage
Plant structure DEvelopment stage (PDE)	shoot system development stage	1	0.04053	--	INHERITED FROM: phyllome development stage || reproductive shoot system development stage || floral organ formation stage || floral organ differentiation stage || flowering stage || corolla development stage || plant organ development stage || 4 leaf senescence stage
Plant structure DEvelopment stage (PDE)	sporophyte development stage	1	0.2022	--	INHERITED FROM: LP.08 eight leaves visible stage || LP.10 ten leaves visible stage || LP.06 six leaves visible stage || sporophyte vegetative stage || leaf production stage || 1 main shoot growth stage || LP.04 four leaves visible stage
Plant structure DEvelopment stage (PDE)	4 leaf senescence stage	0	0.478	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.04 four leaves visible stage	0	0.4338	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.08 eight leaves visible stage	0	0.586	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.10 ten leaves visible stage	0	0.513	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.06 six leaves visible stage	0	0.5243	Least Informative	DIRECT

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Enzyme Commission (EC)

Highlighted in gray are those with FDR_all>0.001

	EC term	FDR (all)	IC level	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Transferases	0	0.3035	--	DIRECT
Enzyme Commission (EC)	Methyltransferases	0	1.181	--	DIRECT
Enzyme Commission (EC)	Homocysteine S-methyltransferase	0	2.952	--	DIRECT
Enzyme Commission (EC)	Methionine synthase	0	2.253	--	DIRECT
Enzyme Commission (EC)	Betaine--homocysteine S-methyltransferase	0	2.952	--	DIRECT
Enzyme Commission (EC)	Transferring one-carbon groups	0	1.054	Moderately Informative	DIRECT

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InterPro annotation

• Cross references: IPR003726 SSF82282 Protein matches
• Abstract: S-methylmethionine: homocysteine methyltransferase from Escherichia coli accepts selenohomocysteine as a substrate. S-methylmethionine is an abundant plant product that can be utilised for methionine biosynthesis [9882684]. Human methionine synthase (5-methyltetrahydrofolate:L-homocysteine S-transmethylase) shares 53 and 63% identity with the E. coli and the presumptive Caenorhabditis elegans proteins, respectively, and contains all residues implicated in B12 binding to the E. coli protein [9013615]. Betaine--homocysteine S-methyltransferase converts betaine and homocysteine to dimethylglycine and methionine, respectively. This reaction is also required for the irreversible oxidation of choline [8798461].

InterPro database

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