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 (1,677) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,444 21,485 34
Proteins 9,185 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 process0.011671Least InformativeInherited
Biological Process (BP)response to stimulus0.190.8217Least InformativeInherited
Biological Process (BP)protein metabolic process01Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.000000028611Least InformativeInherited
Biological Process (BP)cellular protein modification process00.000006729Moderately InformativeDirect
Biological Process (BP)regulation of cellular component organization0.02980.867Moderately InformativeInherited
Biological Process (BP)regulation of localization0.17850.2035Moderately InformativeInherited
Biological Process (BP)immune system process0.10680.2688Moderately InformativeInherited
Biological Process (BP)positive regulation of response to stimulus0.30350.003991Moderately InformativeInherited
Biological Process (BP)regulation of immune effector process0.00010460.0000003402InformativeDirect
Biological Process (BP)regulation of response to external stimulus0.00062550.00000006968InformativeDirect
Biological Process (BP)positive regulation of transport0.0071760.00003632InformativeInherited
Biological Process (BP)positive regulation of cellular component organization0.0073980.06352InformativeInherited
Biological Process (BP)immune response0.030060.0008419InformativeInherited
Biological Process (BP)immune effector process0.0013990.0000001132InformativeInherited
Biological Process (BP)regulation of response to stress0.058360.00169InformativeInherited
Biological Process (BP)positive regulation of immune system process0.018940.000003276InformativeInherited
Biological Process (BP)regulation of immune response0.051270.00001482InformativeInherited
Biological Process (BP)activation of immune response0.00054170.0000000004096Highly InformativeDirect
Biological Process (BP)regulation of acute inflammatory response0.00000027620Highly InformativeDirect
Biological Process (BP)humoral immune response0.00032430.0000000000004402Highly InformativeDirect
Biological Process (BP)regulation of endocytosis0.0001820.00001818Highly InformativeDirect
Biological Process (BP)protein activation cascade0.0023510Highly InformativeInherited
Molecular Function (MF)binding0.000000068481Least InformativeInherited
Molecular Function (MF)cation binding00Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups00InformativeDirect
Molecular Function (MF)enzyme binding0.00000019080.006203InformativeInherited
Molecular Function (MF)transition metal ion binding00.02045InformativeInherited
Molecular Function (MF)prenyltransferase activity00Highly InformativeDirect
Molecular Function (MF)Ras GTPase binding10.000000008421Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.54631Least InformativeInherited
Cellular Component (CC)protein complex00.1729Least InformativeInherited
Cellular Component (CC)CAAX-protein geranylgeranyltransferase complex00Highly InformativeDirect
Cellular Component (CC)protein farnesyltransferase complex0.000000000014750Highly 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 0.000001113 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0000001491 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 0.8217 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 0.000006729 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.00000006031 Moderately Informative Direct
Biological Process (BP) lipid biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.000006894 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.02499 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.01547 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.7102 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.867 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.2035 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.1018 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.004452 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.004814 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.08299 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.03884 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 signal transduction 0.9356 Moderately Informative Inherited
Biological Process (BP) immune system process 0.2688 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.001265 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.003991 Moderately Informative Inherited
Biological Process (BP) immune effector process 0.0000001132 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.000003276 Informative Direct
Biological Process (BP) regulation of immune effector process 0.0000003402 Informative Direct
Biological Process (BP) alcohol metabolic process 0.000000000001238 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 0.0008419 Informative Direct
Biological Process (BP) response to wounding 0.0001836 Informative Direct
Biological Process (BP) response to hormone stimulus 0.000007035 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.00000006968 Informative Direct
Biological Process (BP) regulation of immune response 0.00001482 Informative Direct
Biological Process (BP) positive regulation of transport 0.00003632 Informative Direct
Biological Process (BP) regulation of peptidase activity 0.0002271 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0.000003976 Informative Direct
Biological Process (BP) response to other organism 0.01245 Informative Inherited
Biological Process (BP) negative regulation of catalytic activity 0.02627 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.06352 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.7934 Informative Inherited
Biological Process (BP) regulation of response to stress 0.00169 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.001422 Informative Inherited
Biological Process (BP) lipid catabolic process 0.2074 Informative Inherited
Biological Process (BP) organophosphate catabolic process 0.5446 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.07356 Informative Inherited
Biological Process (BP) activation of immune response 0.0000000004096 Highly Informative Direct
Biological Process (BP) regulation of acute inflammatory response 0 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 0.000000009255 Highly Informative Direct
Biological Process (BP) steroid biosynthetic process 0.00000004019 Highly Informative Direct
Biological Process (BP) phagocytosis 0.000002542 Highly Informative Direct
Biological Process (BP) humoral immune response 0.0000000000004402 Highly Informative Direct
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.0000003431 Highly Informative Direct
Biological Process (BP) isoprenoid biosynthetic process 0 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 0.000000007165 Highly Informative Direct
Biological Process (BP) sterol metabolic process 0.000000007657 Highly Informative Direct
Biological Process (BP) regulation of endocytosis 0.00001818 Highly Informative Direct
Biological Process (BP) alcohol biosynthetic process 0.00000000000002099 Highly Informative Direct
Biological Process (BP) regulation of protein processing 0.0000000000002677 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 0.02229 Moderately Informative Inherited
Molecular Function (MF) enzyme inhibitor activity 0.00000006442 Informative Direct
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0 Informative Direct
Molecular Function (MF) peptidase regulator activity 0.000000001909 Informative Direct
Molecular Function (MF) receptor binding 0.04383 Informative Inherited
Molecular Function (MF) enzyme binding 0.006203 Informative Inherited
Molecular Function (MF) transition metal ion binding 0.02045 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 0.000000008421 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 0.1729 Least Informative Inherited
Cellular Component (CC) extracellular region part 0.1774 Moderately Informative Inherited
Cellular Component (CC) plastid 0.00005909 Informative Direct
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 0.0000001413 Highly Informative Direct
Cellular Component (CC) blood microparticle 0.000002049 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)urinary system disease0.01591Moderately InformativeInherited
Disease Ontology (DO)skin disease0.01635Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.1148Moderately InformativeInherited
Disease Ontology (DO)periodontitis0.0001904InformativeDirect
Disease Ontology (DO)psoriasis0.0007069InformativeDirect
Disease Ontology (DO)proteinuria0.00001859Highly 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 phenotype0.002047Least InformativeInherited
Mammalian Phenotype (MP)mortality/aging0.2872Least InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.001087Moderately InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.004839Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system physiology0.1782Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.001643InformativeInherited
Mammalian Phenotype (MP)abnormal placenta morphology0.007482InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.02885InformativeInherited
Mammalian Phenotype (MP)abnormal hepatobiliary system physiology0.04644InformativeInherited
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.0005511Highly InformativeDirect
Mammalian Phenotype (MP)abnormal trophoblast layer morphology0.0005563Highly InformativeDirect
Mammalian Phenotype (MP)abnormal pregnancy0.0005563Highly InformativeDirect
Mammalian Phenotype (MP)abnormal placenta labyrinth morphology0.0007683Highly 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 system0.03358Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.8619Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.4535Moderately InformativeInherited
Xenopus ANatomical entity (XAN)midgut0.000001241Highly InformativeDirect
Xenopus ANatomical entity (XAN)hindgut0.000004583Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.0002569Highly 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)0.00000000000003069InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Diphosphoric monoester hydrolases0.0000000006754Highly 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 metabolism0.01637Moderately InformativeInherited
Biological processInflammatory response0InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processPlant defense0InformativeDirect
Biological processLipid biosynthesis0.5003InformativeInherited
Biological processComplement pathway0Highly InformativeDirect
Biological processSteroid biosynthesis0Highly InformativeDirect
Biological processComplement alternate pathway0.0000000001395Highly InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentSecreted0.00000002401Moderately InformativeDirect
Cellular componentChloroplast0InformativeDirect
DomainRepeat0.0003471Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionPotassium0.00008516InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationToxin0.4499InformativeInherited
Post-translational modificationGlycoprotein0.0001135Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0.00000000000002334Moderately InformativeDirect
Post-translational modificationSulfation0.000001148InformativeDirect
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 metabolism0.2848Moderately InformativeInherited
UniPathway (UP)lipid biosynthesis1Moderately InformativeInherited
UniPathway (UP)terpene metabolism0InformativeDirect
UniPathway (UP)plant hormone metabolism0.00000000006546InformativeDirect
UniPathway (UP)alkaloid metabolism0.00001992InformativeDirect
UniPathway (UP)plant hormone biosynthesis0.000000000002963Highly InformativeDirect
UniPathway (UP)monoterpene metabolism0.09165Highly InformativeInherited

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 ]