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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 (3,173) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,572 58,639 12
Proteins 11,360 58,036 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 process0.00004780.0000006634Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.15780.09931Least InformativeInherited
Biological Process (BP)single-organism cellular process0.76871Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.054370.005231Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.1070.01584Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.017220.00009707Least InformativeInherited
Biological Process (BP)macromolecule metabolic process0.83851Least InformativeInherited
Biological Process (BP)primary metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.085080.007701Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.055370.004639Least InformativeInherited
Biological Process (BP)cofactor metabolic process0.00042830.000000003342Moderately InformativeDirect
Biological Process (BP)cellular protein modification process0.001370.1242Moderately InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.0000045120.0003002InformativeDirect
Biological Process (BP)tetrapyrrole metabolic process0.000000000012830InformativeDirect
Biological Process (BP)pigment metabolic process0.000060830.00000001402InformativeDirect
Biological Process (BP)heme biosynthetic process0.000035810.00000001098Highly InformativeDirect
Molecular Function (MF)transferase activity0.000000000017960.0000000004054Least InformativeDirect
Molecular Function (MF)transferase activity, transferring one-carbon groups00InformativeDirect
Molecular Function (MF)S-adenosylmethionine-dependent methyltransferase activity0.29020.1327Highly 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 0.0000006634 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.00009707 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.01584 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.09931 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.005231 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.007701 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.004639 Least Informative Inherited
Biological Process (BP) cofactor metabolic process 0.000000003342 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.1242 Moderately Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.0003002 Informative Direct
Biological Process (BP) tetrapyrrole metabolic process 0 Informative Direct
Biological Process (BP) pigment metabolic process 0.00000001402 Informative Direct
Biological Process (BP) heme biosynthetic process 0.00000001098 Highly Informative Direct
Molecular Function (MF) transferase activity 0.0000000004054 Least Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0 Informative Direct
Molecular Function (MF) S-adenosylmethionine-dependent methyltransferase activity 0.1327 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

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)Other lyases1Highly InformativeInherited

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

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cofactor metabolism0Least InformativeDirect
UniPathway (UP)biopolymer metabolism0.00000000002241Least InformativeDirect
UniPathway (UP)amino-acid metabolism0.8512Least InformativeInherited
UniPathway (UP)porphyrin-containing compound metabolism0Moderately InformativeDirect
UniPathway (UP)macrocycle metabolism0Moderately InformativeDirect
UniPathway (UP)adenosylcobalamin biosynthesis0InformativeDirect
UniPathway (UP)nonprotein amino-acid biosynthesis0InformativeDirect
UniPathway (UP)siroheme biosynthesis0Highly InformativeDirect
UniPathway (UP)peptidyl-diphthamide biosynthesis0Highly InformativeDirect

Document: UP 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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]