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Terpenoid cyclases/Protein prenyltransferases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   alpha/alpha toroid [ 48207] (6)
Superfamily:   Terpenoid cyclases/Protein prenyltransferases [ 48239] (4)
Families:   Terpenoid cyclase N-terminal domain [ 48240] (2)
  Terpene synthases [ 48243] (2)
  Protein prenyltransferases [ 48246] (2)
  Complement components [ 48251] (2)


Superfamily statistics
Genomes (1,697) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 12,069 40,672 34
Proteins 9,729 33,784 29


Functional annotation
General category Metabolism
Detailed category Secondary metabolism

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)primary metabolic process0.000000000023860.00001303Least InformativeDirect
Biological Process (BP)macromolecule metabolic process01Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.0000000000000046851Least InformativeInherited
Biological Process (BP)cellular protein modification process00.000000439Moderately InformativeDirect
Molecular Function (MF)binding0.00000047491Least InformativeInherited
Molecular Function (MF)transferase activity01Least InformativeInherited
Molecular Function (MF)metal ion binding00Moderately InformativeDirect
Molecular Function (MF)zinc ion binding00.00004901InformativeDirect
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups00InformativeDirect
Molecular Function (MF)enzyme binding0.00000025050.04392InformativeInherited
Molecular Function (MF)prenyltransferase activity00Highly InformativeDirect
Molecular Function (MF)small GTPase binding00.00000007721Highly InformativeDirect
Cellular Component (CC)cytoplasmic part0.56131Least InformativeInherited
Cellular Component (CC)transferase complex00Moderately InformativeDirect
Cellular Component (CC)CAAX-protein geranylgeranyltransferase complex00Highly InformativeDirect
Cellular Component (CC)protein farnesyltransferase complex0.000000000010140Highly InformativeDirect
Cellular Component (CC)Rab-protein geranylgeranyltransferase complex00Highly InformativeDirect

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 0.0000002084 Least Informative Direct
Biological Process (BP) primary metabolic process 0.00001303 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.239 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.3867 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0.000000439 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) defense response 0.0001951 Moderately Informative Direct
Biological Process (BP) response to biotic stimulus 0.00000001411 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.01169 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.01123 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.007728 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.03778 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.5113 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.738 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.09909 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.1223 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.08857 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.4133 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.5189 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.2103 Moderately Informative Inherited
Biological Process (BP) immune system process 0.1035 Moderately Informative Inherited
Biological Process (BP) response to acid chemical 0.000002948 Informative Direct
Biological Process (BP) immune effector process 0.000009837 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.00002556 Informative Direct
Biological Process (BP) phospholipid metabolic process 0 Informative Direct
Biological Process (BP) isoprenoid metabolic process 0 Informative Direct
Biological Process (BP) immune response 0.0002097 Informative Direct
Biological Process (BP) response to wounding 0.00005827 Informative Direct
Biological Process (BP) regulation of proteolysis 0.0001895 Informative Direct
Biological Process (BP) organophosphate catabolic process 0.00004096 Informative Direct
Biological Process (BP) regulation of immune response 0.0002618 Informative Direct
Biological Process (BP) alcohol metabolic process 0.00867 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.09854 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.5164 Informative Inherited
Biological Process (BP) regulation of defense response 0.001084 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.001055 Informative Inherited
Biological Process (BP) positive regulation of transport 0.01957 Informative Inherited
Biological Process (BP) lipid catabolic process 0.4405 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.002549 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.003356 Informative Inherited
Biological Process (BP) regulation of acute inflammatory response 0.0000000002805 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 0.000001681 Highly Informative Direct
Biological Process (BP) phagocytosis 0.00000005256 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.0000006059 Highly Informative Direct
Biological Process (BP) isoprenoid biosynthetic process 0 Highly Informative Direct
Biological Process (BP) phospholipid catabolic process 0.0006452 Highly Informative Direct
Biological Process (BP) response to estrogen 0.00006421 Highly Informative Direct
Biological Process (BP) alcohol biosynthetic process 0.000005428 Highly Informative Direct
Biological Process (BP) regulation of protein processing 0.00003364 Highly Informative Direct
Biological Process (BP) secondary alcohol metabolic process 0.0003574 Highly Informative Direct
Biological Process (BP) regulation of lipid localization 0.00002513 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0 Moderately Informative Direct
Molecular Function (MF) molecular function regulator 0.2979 Moderately Informative Inherited
Molecular Function (MF) enzyme inhibitor activity 0.00002239 Informative Direct
Molecular Function (MF) zinc ion binding 0.00004901 Informative Direct
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0 Informative Direct
Molecular Function (MF) peptidase regulator activity 0.000001057 Informative Direct
Molecular Function (MF) receptor binding 0.04925 Informative Inherited
Molecular Function (MF) enzyme binding 0.04392 Informative Inherited
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.1338 Informative Inherited
Molecular Function (MF) G-protein coupled receptor binding 0.0000001813 Highly Informative Direct
Molecular Function (MF) prenyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) carbon-oxygen lyase activity, acting on phosphates 0 Highly Informative Direct
Molecular Function (MF) intramolecular transferase activity 0 Highly Informative Direct
Molecular Function (MF) serine hydrolase activity 0.000198 Highly Informative Direct
Molecular Function (MF) small GTPase binding 0.00000007721 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) transferase complex 0 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0.02334 Moderately Informative Inherited
Cellular Component (CC) plastid 0.00001506 Informative Direct
Cellular Component (CC) extracellular space 0.00611 Informative Inherited
Cellular Component (CC) CAAX-protein geranylgeranyltransferase complex 0 Highly Informative Direct
Cellular Component (CC) protein farnesyltransferase complex 0 Highly Informative Direct
Cellular Component (CC) Rab-protein geranylgeranyltransferase complex 0 Highly Informative Direct
Cellular Component (CC) chloroplast stroma 0.0000005799 Highly Informative Direct
Cellular Component (CC) blood microparticle 0.00003427 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Hydro-lyases1Moderately InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited
Enzyme Commission (EC)Transferring other groups0InformativeDirect
Enzyme Commission (EC)Acting on phosphates0InformativeDirect
Enzyme Commission (EC)Intramolecular lyases1InformativeInherited
Enzyme Commission (EC)Protein geranylgeranyltransferase type II0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processImmunity0.00000000001391Moderately InformativeDirect
Biological processLipid metabolism0.02941Moderately InformativeInherited
Biological processInflammatory response0InformativeDirect
Biological processPlant defense0InformativeDirect
Biological processInnate immunity4.848e-16InformativeDirect
Biological processLipid biosynthesis0.4399InformativeInherited
Biological processComplement pathway0Highly InformativeDirect
Biological processSteroid biosynthesis0Highly InformativeDirect
Biological processComplement alternate pathway0.000000000021Highly InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentSecreted0.0000003793Moderately InformativeDirect
Cellular componentChloroplast0InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationToxin0.496InformativeInherited
Post-translational modificationSerine protease inhibitor0Highly InformativeDirect
Post-translational modificationGlycoprotein0.0006067Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0.00000000000005661Moderately InformativeDirect
Post-translational modificationSulfation0.000002964InformativeDirect
Post-translational modificationThioester bond0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008930 SSF48239 Protein matches
Abstract

Protein prenyltransferases catalyze the transfer of the carbon moiety of C15 farnesyl pyrophosphate or geranylgeranyl pyrophosphate synthase to a conserved cysteine residue in a CaaX motif of protein and peptide substrates. The addition of a farnesyl group is required to anchor proteins to the cell membrane. In the 3D structure of a mammalian Ras farnesyltransferases (Ftase), both subunits are largely composed of alpha-helices. The alpha-2 to alpha-15 helices in the alpha subunit fold into a novel helical hairpin structure, resulting in a crescent-shape domain that envelopes part of the subunit. The 12 helices of the beta-subunit form an alpha-alpha barrel. Six additional helices connect the inner core of helices and form the outside of the helical barrel. A deep cleft surrounded by hydrophobic amino acids in the centre of the barrel is proposed as the FPP-binding pocket. A single Zn2+ ion is located at the junction between the hydrophilic surface groove near the subunit interface

Terpenoid cyclases such as squalene cyclase, pentalenene synthase, 5-epi-aristolochene synthase, and trichodiene synthase are responsible for the synthesis of cholesterol, a hydrocarbon precursor of the pentalenolactone family of antibiotics, a precursor of the antifungal phytoalexin capsidiol, and the precursor of antibiotics and mycotoxins, respectively. In the structures of these three enzymes, the similar structural feature referred to as 'terpenoid synthase fold' with 10-12 mostly antiparallel alpha-helices is found, as also observed in protein prenyltransferases. The high structural similarity provides support for the hypothesis that the three families of prenyltransferases have related evolution despite their low sequence similarity [PubMed12135472].


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 12 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 Terpenoid cyclases/Protein prenyltransferases 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 12 hidden Markov models representing the Terpenoid cyclases/Protein prenyltransferases 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 ]