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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 (1,688) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,905 21,485 34
Proteins 9,575 18,690 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)regulation of cellular process0.00069741Least InformativeInherited
Biological Process (BP)response to stimulus0.110.826Least InformativeInherited
Biological Process (BP)protein metabolic process01Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.000000022241Least InformativeInherited
Biological Process (BP)cellular protein modification process00.000006486Moderately InformativeDirect
Biological Process (BP)regulation of cellular component organization0.16950.9921Moderately InformativeInherited
Biological Process (BP)regulation of localization0.27340.2211Moderately InformativeInherited
Biological Process (BP)immune system process0.077230.2606Moderately InformativeInherited
Biological Process (BP)positive regulation of response to stimulus0.046730.0003698Moderately InformativeInherited
Biological Process (BP)regulation of immune effector process0.000079840.0000003176InformativeDirect
Biological Process (BP)positive regulation of transport0.036120.00004309InformativeInherited
Biological Process (BP)positive regulation of cellular component organization0.020630.06896InformativeInherited
Biological Process (BP)regulation of vesicle-mediated transport0.0029850.0006482InformativeInherited
Biological Process (BP)immune response0.028540.0008099InformativeInherited
Biological Process (BP)immune effector process0.0010620.0000001154InformativeInherited
Biological Process (BP)regulation of defense response0.001360.0008767InformativeInherited
Biological Process (BP)regulation of response to external stimulus0.015520.0000001199InformativeInherited
Biological Process (BP)positive regulation of immune system process0.081510.0000037InformativeInherited
Biological Process (BP)regulation of immune response0.27190.00001817InformativeInherited
Biological Process (BP)regulation of acute inflammatory response0.00000022790Highly InformativeDirect
Biological Process (BP)humoral immune response0.00024720.0000000000004558Highly InformativeDirect
Biological Process (BP)regulation of endocytosis0.0000068340.00002063Highly InformativeDirect
Biological Process (BP)protein activation cascade0.0022490Highly InformativeInherited
Molecular Function (MF)binding0.0000000032261Least InformativeInherited
Molecular Function (MF)transferase activity01Least InformativeInherited
Molecular Function (MF)cation binding00Moderately InformativeDirect
Molecular Function (MF)zinc ion binding00.00002577InformativeDirect
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups00InformativeDirect
Molecular Function (MF)enzyme binding0.00000023030.008117InformativeInherited
Molecular Function (MF)prenyltransferase activity00Highly InformativeDirect
Molecular Function (MF)Ras GTPase binding10.00000001242Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.5031Least InformativeInherited
Cellular Component (CC)protein complex00.1326Least 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 0.000001931 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.000000325 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.826 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 0.000006486 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.00000007463 Moderately Informative Direct
Biological Process (BP) lipid biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.000006052 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.0003698 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.02725 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.01865 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.7246 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.9921 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.2211 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.1552 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.006865 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.006231 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.1014 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.0426 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.7324 Moderately Informative Inherited
Biological Process (BP) immune system process 0.2606 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.0031 Moderately Informative Inherited
Biological Process (BP) immune effector process 0.0000001154 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.0000037 Informative Direct
Biological Process (BP) regulation of immune effector process 0.0000003176 Informative Direct
Biological Process (BP) alcohol metabolic process 0.00000000001264 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 0.0008099 Informative Direct
Biological Process (BP) response to wounding 0.0001683 Informative Direct
Biological Process (BP) response to hormone stimulus 0.00001141 Informative Direct
Biological Process (BP) regulation of defense response 0.0008767 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.0000001199 Informative Direct
Biological Process (BP) regulation of immune response 0.00001817 Informative Direct
Biological Process (BP) positive regulation of transport 0.00004309 Informative Direct
Biological Process (BP) regulation of peptidase activity 0.0002318 Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.0006482 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0.00001155 Informative Direct
Biological Process (BP) response to other organism 0.01232 Informative Inherited
Biological Process (BP) negative regulation of catalytic activity 0.02683 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.06896 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.4296 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.001611 Informative Inherited
Biological Process (BP) lipid catabolic process 0.1994 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.5395 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.07807 Informative Inherited
Biological Process (BP) regulation of acute inflammatory response 0 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 0.000000008219 Highly Informative Direct
Biological Process (BP) steroid biosynthetic process 0.0000001306 Highly Informative Direct
Biological Process (BP) phagocytosis 0.000002941 Highly Informative Direct
Biological Process (BP) humoral immune response 0.0000000000004558 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.000000369 Highly Informative Direct
Biological Process (BP) isoprenoid biosynthetic process 0 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 0.000000008091 Highly Informative Direct
Biological Process (BP) sterol metabolic process 0.00000002751 Highly Informative Direct
Biological Process (BP) regulation of endocytosis 0.00002063 Highly Informative Direct
Biological Process (BP) alcohol biosynthetic process 0.0000000000001111 Highly Informative Direct
Biological Process (BP) regulation of protein processing 0.0000000000003027 Highly Informative Direct
Biological Process (BP) protein activation cascade 0 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 0 Moderately Informative Direct
Molecular Function (MF) enzyme regulator activity 0.01927 Moderately Informative Inherited
Molecular Function (MF) enzyme inhibitor activity 0.00000006838 Informative Direct
Molecular Function (MF) zinc ion binding 0.00002577 Informative Direct
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0 Informative Direct
Molecular Function (MF) peptidase regulator activity 0.000000002035 Informative Direct
Molecular Function (MF) receptor binding 0.04543 Informative Inherited
Molecular Function (MF) enzyme binding 0.008117 Informative Inherited
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) Ras GTPase binding 0.00000001242 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 0.1326 Least Informative Inherited
Cellular Component (CC) extracellular region part 0.2095 Moderately Informative Inherited
Cellular Component (CC) plastid 0.00006422 Informative Direct
Cellular Component (CC) extracellular space 0.002079 Informative Inherited
Cellular Component (CC) chloroplast stroma 0.0000001432 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)mouth disease0.0007075Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.01616Moderately InformativeInherited
Disease Ontology (DO)skin disease0.01645Moderately InformativeInherited
Disease Ontology (DO)periodontitis0.0002025InformativeDirect
Disease Ontology (DO)psoriasis0.0007222InformativeDirect
Disease Ontology (DO)proteinuria0.00002171Highly 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 phenotype0.002031Least InformativeInherited
Mammalian Phenotype (MP)mortality/aging0.2869Least InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.001096Moderately InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.004809Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system physiology0.1795Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.001629InformativeInherited
Mammalian Phenotype (MP)abnormal placenta morphology0.007347InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.02898InformativeInherited
Mammalian Phenotype (MP)abnormal hepatobiliary system physiology0.04753InformativeInherited
Mammalian Phenotype (MP)abnormal trophoblast layer morphology0.0005444Highly InformativeDirect
Mammalian Phenotype (MP)abnormal pregnancy0.0005444Highly InformativeDirect
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.0005514Highly InformativeDirect
Mammalian Phenotype (MP)abnormal placenta labyrinth morphology0.0007503Highly 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 variant0.00004012Moderately 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 system0.03368Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.8635Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.4606Moderately InformativeInherited
Xenopus ANatomical entity (XAN)midgut0.000001233Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindgut0.000004555Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.0002736Highly 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)0.00000000000003209InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Diphosphoric monoester hydrolases0.0000000008504Highly 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 metabolism0.01692Moderately InformativeInherited
Biological processInflammatory response0InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processPlant defense0InformativeDirect
Biological processLipid biosynthesis0.4961InformativeInherited
Biological processComplement pathway0Highly InformativeDirect
Biological processSteroid biosynthesis0Highly InformativeDirect
Biological processComplement alternate pathway0.0000000001396Highly InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentSecreted0.00000002429Moderately InformativeDirect
Cellular componentChloroplast0InformativeDirect
DomainRepeat0.0003387Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionPotassium0.00008502InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationToxin0.4613InformativeInherited
Post-translational modificationGlycoprotein0.0001097Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0.00000000000002251Moderately InformativeDirect
Post-translational modificationSulfation0.000001141InformativeDirect
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)secondary metabolite metabolism0Moderately InformativeDirect
UniPathway (UP)hormone metabolism0.00004627Moderately InformativeDirect
UniPathway (UP)plant hormone biosynthesis0.000005396InformativeDirect
UniPathway (UP)terpene biosynthesis0.5418InformativeInherited
UniPathway (UP)terpenoid biosynthesis0Highly InformativeDirect
UniPathway (UP)oleoresin biosynthesis0Highly 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 ]