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 (1,359) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 9,320 13,835 34
Proteins 7,607 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)cellular macromolecule metabolic process0.00057691Least InformativeInherited
Biological Process (BP)response to stimulus0.01570.3161Least InformativeInherited
Biological Process (BP)protein metabolic process1.054e-101Least InformativeInherited
Biological Process (BP)regulation of response to stimulus0.32240.2919Moderately InformativeInherited
Biological Process (BP)cellular protein modification process5.493e-110.06272Moderately InformativeInherited
Biological Process (BP)immune system process0.028220.5197Moderately InformativeInherited
Biological Process (BP)immune effector process0.00052252.117e-05InformativeDirect
Biological Process (BP)regulation of immune effector process2.72e-050.0001948InformativeDirect
Biological Process (BP)positive regulation of immune system process0.022260.0001888InformativeInherited
Biological Process (BP)regulation of response to stress0.021280.08316InformativeInherited
Biological Process (BP)immune response0.028440.01857InformativeInherited
Biological Process (BP)regulation of response to external stimulus0.0032430.0001208InformativeInherited
Biological Process (BP)regulation of immune response0.022810.0002434InformativeInherited
Biological Process (BP)activation of immune response0.00020633.816e-07Highly InformativeDirect
Biological Process (BP)humoral immune response0.00011671.638e-09Highly InformativeDirect
Biological Process (BP)regulation of inflammatory response2.788e-051.042e-05Highly InformativeDirect
Biological Process (BP)protein activation cascade0.0006431.235e-13Highly InformativeDirect
Molecular Function (MF)transferase activity1.155e-111Least InformativeInherited
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups00InformativeDirect
Molecular Function (MF)prenyltransferase activity00Highly InformativeDirect
Cellular Component (CC)protein complex5.729e-061Least 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 4.588e-10 Least Informative Direct
Biological Process (BP) single-organism metabolic process 4.054e-13 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) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.3161 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 9.436e-11 Moderately Informative Direct
Biological Process (BP) lipid biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 1.003e-08 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 7.817e-07 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.1547 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.002215 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.5712 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.02228 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.2919 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.004923 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.06272 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.07207 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.004592 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.05134 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.007619 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.6246 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.6172 Moderately Informative Inherited
Biological Process (BP) immune system process 0.5197 Moderately Informative Inherited
Biological Process (BP) immune effector process 2.117e-05 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.0001888 Informative Direct
Biological Process (BP) regulation of immune effector process 0.0001948 Informative Direct
Biological Process (BP) alcohol metabolic process 7.09e-11 Informative Direct
Biological Process (BP) phospholipid metabolic process 4.008e-15 Informative Direct
Biological Process (BP) isoprenoid metabolic process 0 Informative Direct
Biological Process (BP) steroid metabolic process 2.023e-06 Informative Direct
Biological Process (BP) response to wounding 1.733e-05 Informative Direct
Biological Process (BP) response to hormone stimulus 4.588e-06 Informative Direct
Biological Process (BP) cellular membrane organization 0.0007031 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 0.0004198 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.0001208 Informative Direct
Biological Process (BP) regulation of immune response 0.0002434 Informative Direct
Biological Process (BP) positive regulation of transport 6.527e-05 Informative Direct
Biological Process (BP) response to other organism 0.0001838 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0.0001499 Informative Direct
Biological Process (BP) regulation of hydrolase activity 0.03132 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.02716 Informative Inherited
Biological Process (BP) defense response 0.01192 Informative Inherited
Biological Process (BP) regulation of response to stress 0.08316 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.2757 Informative Inherited
Biological Process (BP) lipid catabolic process 0.5349 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.4724 Informative Inherited
Biological Process (BP) immune response 0.01857 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.05759 Informative Inherited
Biological Process (BP) activation of immune response 3.816e-07 Highly Informative Direct
Biological Process (BP) steroid biosynthetic process 3.969e-06 Highly Informative Direct
Biological Process (BP) phagocytosis 5.701e-06 Highly Informative Direct
Biological Process (BP) humoral immune response 1.638e-09 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 8.112e-07 Highly Informative Direct
Biological Process (BP) isoprenoid biosynthetic process 0 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 2.116e-09 Highly Informative Direct
Biological Process (BP) sterol metabolic process 6.797e-09 Highly Informative Direct
Biological Process (BP) alcohol biosynthetic process 9.65e-12 Highly Informative Direct
Biological Process (BP) regulation of inflammatory response 1.042e-05 Highly Informative Direct
Biological Process (BP) regulation of protein processing 5.032e-07 Highly Informative Direct
Biological Process (BP) protein activation cascade 1.235e-13 Highly Informative Direct
Molecular Function (MF) binding 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) cation binding 7.637e-05 Moderately Informative Direct
Molecular Function (MF) enzyme regulator activity 0.004054 Moderately Informative Inherited
Molecular Function (MF) protein binding 1 Moderately Informative Inherited
Molecular Function (MF) enzyme inhibitor activity 4.658e-09 Informative Direct
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0 Informative Direct
Molecular Function (MF) carbon-oxygen lyase activity 0 Informative Direct
Molecular Function (MF) peptidase regulator activity 1.624e-10 Informative Direct
Molecular Function (MF) receptor binding 0.02146 Informative Inherited
Molecular Function (MF) magnesium ion binding 1.308e-07 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
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 1 Least Informative Inherited
Cellular Component (CC) plastid 3.929e-05 Informative Direct
Cellular Component (CC) chloroplast stroma 7.173e-08 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 disease0.01337Moderately InformativeInherited
Disease Ontology (DO)skin disease0.02306Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.1177Moderately InformativeInherited
Disease Ontology (DO)periodontitis0.0002022InformativeDirect
Disease Ontology (DO)psoriasis0.0006902InformativeDirect
Disease Ontology (DO)proteinuria2.007e-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/aging0.1747Least InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.0004291Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype0.002861Moderately InformativeInherited
Mammalian Phenotype (MP)embryogenesis phenotype0.06335Moderately InformativeInherited
Mammalian Phenotype (MP)increased inflammatory response0.000156InformativeDirect
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.0005836InformativeDirect
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.01906InformativeInherited
Mammalian Phenotype (MP)abnormal hepatobiliary system physiology0.0444InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.1271InformativeInherited
Mammalian Phenotype (MP)abnormal pregnancy0.0003243Highly InformativeDirect
Mammalian Phenotype (MP)abnormal trophoblast layer morphology0.0004688Highly InformativeDirect
Mammalian Phenotype (MP)abnormal placenta labyrinth morphology0.0005547Highly 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 system0.03325Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.8457Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.4058Moderately InformativeInherited
Xenopus ANatomical entity (XAN)midgut1.271e-06Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindgut4.707e-06Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.0001338Highly 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)androecium1Least InformativeInherited
Plant ANatomical entity (PAN)gynoecium1Least InformativeInherited
Plant ANatomical entity (PAN)stalk1Least InformativeInherited
Plant ANatomical entity (PAN)filament0.0002356Highly 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)7.017e-15InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Diphosphoric monoester hydrolases8.297e-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 metabolism0.01219Moderately InformativeInherited
Biological processInflammatory response0InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processPlant defense0InformativeDirect
Biological processLipid biosynthesis0.5211InformativeInherited
Biological processComplement pathway0Highly InformativeDirect
Biological processSteroid biosynthesis0Highly InformativeDirect
Biological processComplement alternate pathway1.496e-12Highly InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentSecreted5.738e-08Moderately InformativeDirect
Cellular componentChloroplast0Highly InformativeDirect
DomainRepeat0.0009773Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionPotassium3.267e-05InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationGlycoprotein0.0001068Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues9.815e-10Moderately InformativeDirect
Post-translational modificationSulfation1.026e-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 metabolism1Least InformativeInherited
UniPathway (UP)secondary metabolite metabolism0Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism0.2565Moderately InformativeInherited
UniPathway (UP)lipid biosynthesis1Moderately InformativeInherited
UniPathway (UP)terpene metabolism0InformativeDirect
UniPathway (UP)hormone metabolism7.133e-10InformativeDirect
UniPathway (UP)alkaloid metabolism1.01e-05InformativeDirect
UniPathway (UP)plant hormone biosynthesis1.876e-12Highly 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 ]