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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)


Superfamily statistics
Genomes (3,177) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 11,577 68,332 12
Proteins 11,365 67,220 12


Functional annotation
General category Metabolism
Detailed category Transferases

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)biosynthetic process0.00003630.00000009353Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.0000011420.00006907Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.15590.0279Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.050480.008643Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.051470.007623Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.087890.01432Least InformativeInherited
Biological Process (BP)primary metabolic process11Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.85521Least InformativeInherited
Biological Process (BP)biological regulation0.13821Least InformativeInherited
Biological Process (BP)single-organism cellular process0.60730.9324Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.084660.01776Least InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.00074620.00003326Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process0.00038730.000000006955Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.0000016930.0000005355Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.0024660.00006455Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process0.000084360.1677Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.0018960.0976Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.0002090.2281Moderately InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process0.000043810.1353Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process0.000054670.01116Moderately InformativeInherited
Biological Process (BP)posttranscriptional regulation of gene expression0.0000000035650.00000326InformativeDirect
Biological Process (BP)peptidyl-amino acid modification0.000007470.0001875InformativeDirect
Biological Process (BP)tetrapyrrole metabolic process0.000000000340InformativeDirect
Biological Process (BP)regulation of cellular amide metabolic process0.0000000018250.000001534InformativeDirect
Biological Process (BP)pigment metabolic process0.000055430.00000003945InformativeDirect
Biological Process (BP)heme biosynthetic process0.000031980.00000001719Highly InformativeDirect
Molecular Function (MF)transferase activity0.00000000004350.00000000004384Least InformativeDirect
Molecular Function (MF)transferase activity, transferring one-carbon groups00InformativeDirect
Molecular Function (MF)S-adenosylmethionine-dependent methyltransferase activity0.31340.149Highly InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biosynthetic process 0.00000009353 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.00006907 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.0279 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.008643 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.007623 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.01432 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.9324 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.01776 Least Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.00006455 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.00003326 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.000000006955 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0000005355 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.1353 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.1677 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.0976 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.2281 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.01116 Moderately Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.00000326 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.0001875 Informative Direct
Biological Process (BP) tetrapyrrole metabolic process 0 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.000001534 Informative Direct
Biological Process (BP) pigment metabolic process 0.00000003945 Informative Direct
Biological Process (BP) heme biosynthetic process 0.00000001719 Highly Informative Direct
Molecular Function (MF) transferase activity 0.00000000004384 Least Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0 Informative Direct
Molecular Function (MF) S-adenosylmethionine-dependent methyltransferase activity 0.149 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0Least InformativeDirect
Enzyme Commission (EC)Acting on the CH-CH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Methyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Sole sub-subclass for lyases that do not belong in1InformativeInherited
Enzyme Commission (EC)Sirohydrochlorin ferrochelatase0Highly InformativeDirect
Enzyme Commission (EC)Uroporphyrinogen-III C-methyltransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processrRNA processing0InformativeDirect
Biological processCobalamin biosynthesis0Highly InformativeDirect
Biological processPorphyrin biosynthesis0Highly InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionS-adenosyl-L-methionine0InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationMethyltransferase0InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000878 SSF53790 Protein matches
Abstract

Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway [PubMed11215515]. 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 [PubMed17227226].

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 [PubMed15522295].
  • 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 [PubMed17229157]. 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 [PubMed16866557].
  • 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 [PubMed14595395].
  • 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


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 10 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Tetrapyrrole methylase domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 10 hidden Markov models representing the Tetrapyrrole methylase superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]