Tetrapyrrole methylase superfamily

SCOP classification

• Root: SCOP hierarchy in SUPERFAMILY [ 0] (11)
• Class: Alpha and beta proteins (a/b) [ 51349] (147)
• Fold: Tetrapyrrole methylase [ 53789]
• Superfamily: Tetrapyrrole methylase [ 53790]
• Families: Tetrapyrrole methylase [ 53791] (7)

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Superfamily statistics

	Genomes (3,179)	Uniprot 2018_03 genome	PDB chains (SCOP 1.75)
Domains	11,580	90,291	12
Proteins	11,368	88,892	12

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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)	Other lyases	0	1.715	--	DIRECT
Enzyme Commission (EC)	Transferases	0	0	--	DIRECT
Enzyme Commission (EC)	16S rRNA (cytidine(1402)-2'-O)-methyltransferase	0	2.56	--	DIRECT
Enzyme Commission (EC)	With NAD(+) or NADP(+) as acceptor	0	1.198	--	DIRECT
Enzyme Commission (EC)	Diphthine synthase	0	2.56	--	DIRECT
Enzyme Commission (EC)	Precorrin-2 dehydrogenase	0	2.259	--	DIRECT
Enzyme Commission (EC)	Precorrin-4 C(11)-methyltransferase	0.00000001689	2.56	--	DIRECT
Enzyme Commission (EC)	Oxidoreductases	0	0.2975	Least Informative	DIRECT
Enzyme Commission (EC)	Lyases	0	0.4169	Least Informative	DIRECT
Enzyme Commission (EC)	Transferring one-carbon groups	0	0.7211	Least Informative	DIRECT
Enzyme Commission (EC)	Acting on the CH-CH group of donors	0	1.055	Moderately Informative	DIRECT
Enzyme Commission (EC)	Methyltransferases	0	0.8609	Moderately Informative	DIRECT
Enzyme Commission (EC)	Sole sub-subclass for lyases that do not belong in	1	1.715	Informative	INHERITED FROM: Sirohydrochlorin ferrochelatase
Enzyme Commission (EC)	Sirohydrochlorin ferrochelatase	0	2.083	Highly Informative	DIRECT
Enzyme Commission (EC)	Uroporphyrinogen-III C-methyltransferase	0	2.083	Highly 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)	plant embryo	0	0.5969	--	DIRECT
Plant ANatomical entity (PAN)	stalk	0	0.7019	--	DIRECT
Plant ANatomical entity (PAN)	leaf lamina	0	0.7057	--	DIRECT
Plant ANatomical entity (PAN)	petiole	0	0.7287	--	DIRECT
Plant ANatomical entity (PAN)	stem internode	0	0.6495	--	DIRECT
Plant ANatomical entity (PAN)	inflorescence branch	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	stamen	0	0.6028	--	DIRECT
Plant ANatomical entity (PAN)	phyllome apex	0	0.7019	--	DIRECT
Plant ANatomical entity (PAN)	epidermal cell	0	0.2569	--	DIRECT
Plant ANatomical entity (PAN)	stem	0	0.577	--	DIRECT
Plant ANatomical entity (PAN)	shoot epidermis	0	0.2691	--	DIRECT
Plant ANatomical entity (PAN)	perianth	0	0.5448	--	DIRECT
Plant ANatomical entity (PAN)	cardinal organ part	0	0.51	--	DIRECT
Plant ANatomical entity (PAN)	phyllome	0	0.3809	--	DIRECT
Plant ANatomical entity (PAN)	shoot internode	0	0.6463	--	DIRECT
Plant ANatomical entity (PAN)	corolla	0	0.594	--	DIRECT
Plant ANatomical entity (PAN)	cauline leaf	0	0.7019	--	DIRECT
Plant ANatomical entity (PAN)	lamina	0	0.7057	--	DIRECT
Plant ANatomical entity (PAN)	sporophyll	0	0.4713	--	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)	reproductive shoot system	0	0.4141	--	DIRECT
Plant ANatomical entity (PAN)	androecium	0	0.594	--	DIRECT
Plant ANatomical entity (PAN)	epidermis	0	0.2464	--	DIRECT
Plant ANatomical entity (PAN)	plant cell	0	0.1489	--	DIRECT
Plant ANatomical entity (PAN)	inflorescence axis	0	0.6366	--	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)	pedicel	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	leaf lamina base	0	0.7094	--	DIRECT
Plant ANatomical entity (PAN)	calyx	0	0.5715	--	DIRECT
Plant ANatomical entity (PAN)	petal	0	0.594	--	DIRECT
Plant ANatomical entity (PAN)	plant organ	0	0.2816	--	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)	root	0	0.5579	--	DIRECT
Plant ANatomical entity (PAN)	multi-tissue plant structure	0	0.2691	--	DIRECT
Plant ANatomical entity (PAN)	shoot apex	0	0.5633	--	DIRECT
Plant ANatomical entity (PAN)	collective leaf structure	0	0.55	--	DIRECT
Plant ANatomical entity (PAN)	stomatal complex	0	0.2774	--	DIRECT
Plant ANatomical entity (PAN)	sepal	0	0.5715	--	DIRECT
Plant ANatomical entity (PAN)	vascular leaf	0	0.5246	--	DIRECT
Plant ANatomical entity (PAN)	branch	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	organ lamina	1	0.7057	--	INHERITED FROM: leaf lamina base || leaf lamina
Plant ANatomical entity (PAN)	collective plant organ structure	1	0.04502	--	INHERITED FROM: inflorescence axis || calyx || flower || sporophyll || root system || inflorescence || root || perianth || stem || leaf || phyllome || shoot internode || sepal || vascular leaf || petiole || petal || reproductive shoot system || shoot apex || leaf apex || collective phyllome structure || guard cell || cauline leaf || microsporophyll || leaf lamina || shoot epidermal cell || corolla || pedicel || androecium || stomatal complex || phyllome apex || cotyledon || stamen || stem internode || inflorescence branch || shoot axis || shoot system || leaf lamina base || collective leaf structure || branch || shoot epidermis
Plant ANatomical entity (PAN)	plant structure	1	0	--	INHERITED FROM: perianth || root || sporophyll || calyx || inflorescence axis || flower || lamina || collective plant structure || plant embryo || leaf || shoot internode || phyllome || cardinal organ part || multi-tissue plant structure || microsporophyll || guard cell || cauline leaf || reproductive shoot system || shoot apex || leaf apex || leaf lamina base || branch || collective leaf structure || stem internode || inflorescence branch || shoot system || portion of plant tissue || stomatal complex || plant organ || stem || whole plant || epidermis || root system || inflorescence || cardinal part of multi-tissue plant structure || petiole || stalk || vascular leaf || sepal || epidermal cell || leaf lamina || shoot epidermal cell || corolla || plant axis || collective phyllome structure || petal || plant cell || seed || shoot epidermis || phyllome apex || cotyledon || stamen || shoot axis || pedicel || androecium
Plant ANatomical entity (PAN)	phyllome lamina	1	0.7057	--	INHERITED FROM: leaf lamina base || leaf lamina
Plant ANatomical entity (PAN)	leaf	0	0.5053	Least Informative	DIRECT
Plant ANatomical entity (PAN)	collective phyllome structure	0	0.4648	Least Informative	DIRECT
Plant ANatomical entity (PAN)	seed	0	0.6087	Least Informative	DIRECT
Plant ANatomical entity (PAN)	guard cell	0	0.2774	Least Informative	DIRECT
Plant ANatomical entity (PAN)	whole plant	0	0.4218	Least Informative	DIRECT
Plant ANatomical entity (PAN)	shoot axis	0	0.4735	Least Informative	DIRECT
Plant ANatomical entity (PAN)	root system	0	0.5346	Least Informative	DIRECT
Plant ANatomical entity (PAN)	cardinal part of multi-tissue plant structure	0	0.5029	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 ANatomical entity (PAN)	inflorescence	0	0.5969	Least Informative	DIRECT
Plant ANatomical entity (PAN)	cotyledon	0	0.7615	Moderately Informative	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)	whole plant development stage	0	0.1968	--	DIRECT
Plant structure DEvelopment stage (PDE)	plant organ development stage	0	0.08108	--	DIRECT
Plant structure DEvelopment stage (PDE)	plant embryo stage	0	0.2833	--	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)	flowering stage	0	0.2162	--	DIRECT
Plant structure DEvelopment stage (PDE)	corolla development stage	0	0.1981	--	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)	reproductive shoot system development stage	0	0.05008	--	DIRECT
Plant structure DEvelopment stage (PDE)	life of whole plant stage	1	0.2022	--	INHERITED FROM: sporophyte vegetative stage || C globular stage || LP.10 ten leaves visible stage || E expanded cotyledon stage || LP.12 twelve leaves visible stage || F mature embryo stage || LP.04 four leaves visible stage || D bilateral stage || LP.02 two leaves visible stage || plant embryo 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.12 twelve leaves visible stage || E expanded cotyledon stage || LP.10 ten leaves visible stage || sporophyte vegetative stage || C globular stage || leaf production stage || 1 main shoot growth stage || D bilateral stage || F mature embryo stage || LP.04 four leaves visible stage || plant embryo stage || LP.02 two leaves visible stage
Plant structure DEvelopment stage (PDE)	D bilateral stage	0	0.3729	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	4 leaf senescence stage	0	0.478	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.02 two leaves visible stage	0	0.5603	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	F mature embryo stage	0	0.4088	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.10 ten leaves visible stage	0	0.513	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	E expanded cotyledon stage	0	0.353	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.12 twelve leaves visible stage	0	0.5666	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	C globular stage	0	0.3937	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)	Acting on the CH-CH group of donors	0	1.35	--	DIRECT
Enzyme Commission (EC)	Precorrin-2 dehydrogenase	0	2.475	--	DIRECT
Enzyme Commission (EC)	Transferases	0	0.3035	--	DIRECT
Enzyme Commission (EC)	Methyltransferases	0	1.181	--	DIRECT
Enzyme Commission (EC)	Uroporphyrinogen-III C-methyltransferase	0	2.475	--	DIRECT
Enzyme Commission (EC)	16S rRNA (cytidine(1402)-2'-O)-methyltransferase	0	2.952	--	DIRECT
Enzyme Commission (EC)	Diphthine methyl ester synthase	0	2.952	--	DIRECT
Enzyme Commission (EC)	Diphthine synthase	0	2.952	--	DIRECT
Enzyme Commission (EC)	Other lyases	0	2.107	--	DIRECT
Enzyme Commission (EC)	Sirohydrochlorin ferrochelatase	0	2.475	--	DIRECT
Enzyme Commission (EC)	Precorrin-4 C(11)-methyltransferase	0.00000001519	2.952	--	DIRECT
Enzyme Commission (EC)	Precorrin-6B C(5,15)-methyltransferase (decarboxylating)	0.000000216	2.952	--	DIRECT
Enzyme Commission (EC)	Precorrin-2 C(20)-methyltransferase	0.000003052	2.952	--	DIRECT
Enzyme Commission (EC)	Cobalt-precorrin-4 methyltransferase	0.000003052	2.952	--	DIRECT
Enzyme Commission (EC)	Cobalt-precorrin-7 (C(5))-methyltransferase	0.000003052	2.952	--	DIRECT
Enzyme Commission (EC)	Oxidoreductases	0	0.6234	Least Informative	DIRECT
Enzyme Commission (EC)	Lyases	0	0.6918	Least Informative	DIRECT
Enzyme Commission (EC)	Transferring one-carbon groups	0	1.054	Moderately Informative	DIRECT
Enzyme Commission (EC)	With NAD(+) or NADP(+) as acceptor	0	1.505	Informative	DIRECT
Enzyme Commission (EC)	Other lyases	1	2.107	Highly Informative	INHERITED FROM: Sirohydrochlorin ferrochelatase

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InterPro annotation

• Cross references: IPR000878 SSF53790 Protein matches
• Abstract:

  Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway [11215515]. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including cobalamin (vitamin B12), haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin [17227226].

  This entry represents several tetrapyrrole methylases, which consist of two non-similar domains. These enzymes catalyse the methylation of their substrates using S-adenosyl-L-methionine as a methyl source. Enzymes in this family include:

  • Uroporphyrinogen III methyltransferase (SUMT), which catalyses the conversion of uroporphyrinogen III to precorrin-2 at the first branch-point of the tetrapyrrole synthesis pathway, directing the pathway towards cobalamin or sirohaem synthesis [15522295].
  • Precorrin-2 C20-methyltransferase CobI/CbiL , which introduces a methyl group at C-20 on precorrin-2 to produce precorrin-3A during cobalamin biosynthesis. This reaction is key to the conversion of a porphyrin-type tetrapyrrole ring to a corrin ring [17229157]. In some species, this enzyme is part of a bifunctional protein.
  • Precorrin-4 C11-methyltransferase CobM/CbiF , which introduces a methyl group at C-11 on precorrin-4 to produce precorrin-5 during cobalamin biosynthesis [16866557].
  • Sirohaem synthase CysG , domains 4 and 5, which synthesizes sirohaem from uroporphyrinogen III, at the first branch-point in the tetrapyrrole biosynthetic pathway, directing the pathway towards sirohaem synthesis [14595395].
  • Diphthine synthase , which carries out the methylation step during the modification of a specific histidine residue of elongation factor 2 (EF-2) during diphthine synthesis.

InterPro database

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