SUPERFAMILY 1.75 HMM library and genome assignments server


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 (1,638) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 9,927 13,835 34
Proteins 8,089 11,795 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)response to stimulus0.059350.646Least InformativeInherited
Biological Process (BP)protein metabolic process01Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process2.383e-071Least InformativeInherited
Biological Process (BP)cellular protein modification process00.000334Moderately InformativeDirect
Biological Process (BP)positive regulation of response to stimulus0.30670.003095Moderately InformativeInherited
Biological Process (BP)immune system process0.053470.2643Moderately InformativeInherited
Biological Process (BP)immune effector process0.00076259.373e-08InformativeDirect
Biological Process (BP)regulation of immune effector process5.145e-052.858e-07InformativeDirect
Biological Process (BP)regulation of response to external stimulus0.00060414.993e-08InformativeDirect
Biological Process (BP)positive regulation of immune system process0.019242.788e-06InformativeInherited
Biological Process (BP)immune response0.02820.0006404InformativeInherited
Biological Process (BP)regulation of defense response0.0008240.001062InformativeInherited
Biological Process (BP)regulation of immune response0.054211.324e-05InformativeInherited
Biological Process (BP)activation of immune response0.00029913.611e-10Highly InformativeDirect
Biological Process (BP)humoral immune response0.00018163.292e-13Highly InformativeDirect
Biological Process (BP)protein activation cascade0.0018180Highly InformativeInherited
Biological Process (BP)regulation of inflammatory response0.019321.229e-07Highly InformativeInherited
Molecular Function (MF)binding3.14e-111Least InformativeInherited
Molecular Function (MF)cation binding00Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups00InformativeDirect
Molecular Function (MF)enzyme binding1.677e-070.004525InformativeInherited
Molecular Function (MF)transition metal ion binding00.03046InformativeInherited
Molecular Function (MF)prenyltransferase activity00Highly InformativeDirect
Molecular Function (MF)Ras GTPase binding16.071e-09Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.63561Least InformativeInherited
Cellular Component (CC)protein complex00.1412Least InformativeInherited
Cellular Component (CC)CAAX-protein geranylgeranyltransferase complex00Highly InformativeDirect
Cellular Component (CC)protein farnesyltransferase complex1.049e-110Highly 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 1.27e-07 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1.247e-08 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.646 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0.000334 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 3.517e-08 Moderately Informative Direct
Biological Process (BP) lipid biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 2.768e-06 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0.0009134 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.03906 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.01777 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.6896 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.1065 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.3825 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.005112 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.00505 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.1183 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.03445 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.9279 Moderately Informative Inherited
Biological Process (BP) immune system process 0.2643 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.003095 Moderately Informative Inherited
Biological Process (BP) immune effector process 9.373e-08 Informative Direct
Biological Process (BP) positive regulation of immune system process 2.788e-06 Informative Direct
Biological Process (BP) regulation of immune effector process 2.858e-07 Informative Direct
Biological Process (BP) alcohol metabolic process 1.144e-12 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 0.0006404 Informative Direct
Biological Process (BP) steroid metabolic process 3.908e-09 Informative Direct
Biological Process (BP) response to wounding 0.0001967 Informative Direct
Biological Process (BP) response to hormone stimulus 6.48e-06 Informative Direct
Biological Process (BP) regulation of response to external stimulus 4.993e-08 Informative Direct
Biological Process (BP) regulation of immune response 1.324e-05 Informative Direct
Biological Process (BP) positive regulation of transport 0.000388 Informative Direct
Biological Process (BP) regulation of peptidase activity 0.0002037 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 4.082e-06 Informative Direct
Biological Process (BP) negative regulation of catalytic activity 0.02368 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.7909 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.001327 Informative Inherited
Biological Process (BP) lipid catabolic process 0.2079 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.5352 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.1145 Informative Inherited
Biological Process (BP) regulation of defense response 0.001062 Informative Inherited
Biological Process (BP) activation of immune response 3.611e-10 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 7.965e-09 Highly Informative Direct
Biological Process (BP) steroid biosynthetic process 5.409e-08 Highly Informative Direct
Biological Process (BP) phagocytosis 1.421e-05 Highly Informative Direct
Biological Process (BP) humoral immune response 3.292e-13 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 3.252e-07 Highly Informative Direct
Biological Process (BP) isoprenoid biosynthetic process 0 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 6.237e-09 Highly Informative Direct
Biological Process (BP) sterol metabolic process 7.448e-09 Highly Informative Direct
Biological Process (BP) alcohol biosynthetic process 2.78e-14 Highly Informative Direct
Biological Process (BP) regulation of inflammatory response 1.229e-07 Highly Informative Direct
Biological Process (BP) regulation of protein processing 1.297e-13 Highly Informative Direct
Biological Process (BP) protein activation cascade 0 Highly Informative Direct
Molecular Function (MF) binding 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) cation binding 0 Moderately Informative Direct
Molecular Function (MF) enzyme regulator activity 0.01643 Moderately Informative Inherited
Molecular Function (MF) enzyme inhibitor activity 4.821e-08 Informative Direct
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0 Informative Direct
Molecular Function (MF) peptidase regulator activity 1.491e-09 Informative Direct
Molecular Function (MF) receptor binding 0.08755 Informative Inherited
Molecular Function (MF) enzyme binding 0.004525 Informative Inherited
Molecular Function (MF) transition metal ion binding 0.03046 Informative Inherited
Molecular Function (MF) prenyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) intramolecular transferase activity 0 Highly Informative Direct
Molecular Function (MF) Ras GTPase binding 6.071e-09 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.1412 Least Informative Inherited
Cellular Component (CC) extracellular region part 0.07888 Moderately Informative Inherited
Cellular Component (CC) plastid 8.234e-05 Informative Direct
Cellular Component (CC) extracellular space 0.001523 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 1.425e-07 Highly Informative Direct
Cellular Component (CC) blood microparticle 4.494e-06 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

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)kidney disease0.01308Moderately InformativeInherited
Disease Ontology (DO)skin disease0.01643Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.1153Moderately InformativeInherited
Disease Ontology (DO)periodontitis0.0001905InformativeDirect
Disease Ontology (DO)psoriasis0.000708InformativeDirect
Disease Ontology (DO)proteinuria1.86e-05Highly InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)immune system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0.1615Least InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.0003603Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype0.002191Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system physiology0.1345Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.0004721InformativeDirect
Mammalian Phenotype (MP)abnormal placenta morphology0.005061InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.01932InformativeInherited
Mammalian Phenotype (MP)abnormal hepatobiliary system physiology0.04614InformativeInherited
Mammalian Phenotype (MP)abnormal pregnancy0.0003531Highly InformativeDirect
Mammalian Phenotype (MP)abnormal trophoblast layer morphology0.0003625Highly InformativeDirect
Mammalian Phenotype (MP)abnormal placenta labyrinth morphology0.0004997Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.004687Least InformativeInherited
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect
Worm Phenotype (WP)cell death variant4.012e-05Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0.03347Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.8584Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.442Moderately InformativeInherited
Xenopus ANatomical entity (XAN)midgut1.081e-06Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindgut4.614e-06Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.0001941Highly InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)megasporophyll1Least InformativeInherited
Plant ANatomical entity (PAN)microsporophyll1Least InformativeInherited
Plant ANatomical entity (PAN)flower1Least InformativeInherited
Plant ANatomical entity (PAN)collective phyllome structure1Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure1Least InformativeInherited
Plant ANatomical entity (PAN)filament0.00017Highly InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular transferases (mutases)3.207e-14InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Acting on phosphates0Highly InformativeDirect
Enzyme Commission (EC)Diphosphoric monoester hydrolases9.075e-10Highly InformativeDirect
Enzyme Commission (EC)Intramolecular lyases1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0.01651Moderately InformativeInherited
Biological processInflammatory response0InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processPlant defense0InformativeDirect
Biological processLipid biosynthesis0.5026InformativeInherited
Biological processComplement pathway0Highly InformativeDirect
Biological processSteroid biosynthesis0Highly InformativeDirect
Biological processComplement alternate pathway1.823e-10Highly InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentSecreted1.87e-08Moderately InformativeDirect
Cellular componentChloroplast0InformativeDirect
DomainRepeat0.0003621Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionPotassium8.989e-05InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationToxin0.4411InformativeInherited
Post-translational modificationGlycoprotein0.0001049Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues2.332e-14Moderately InformativeDirect
Post-translational modificationSulfation1.17e-06InformativeDirect
Post-translational modificationThioester bond0Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)lipid metabolism0.505Least InformativeInherited
UniPathway (UP)secondary metabolite metabolism0Moderately InformativeDirect
UniPathway (UP)lipid biosynthesis0.1492Moderately InformativeInherited
UniPathway (UP)terpene metabolism0InformativeDirect
UniPathway (UP)plant hormone biosynthesis2.715e-05InformativeDirect
UniPathway (UP)terpenoid biosynthesis0Highly InformativeDirect
UniPathway (UP)oleoresin biosynthesis9.953e-08Highly InformativeDirect
UniPathway (UP)lanosterol biosynthesis0.0006419Highly InformativeDirect

Document: UP 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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · 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 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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]