SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


Terpenoid cyclases/Protein prenyltransferases superfamily

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


Superfamily statistics
Genomes (1,697) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 12,069 51,943 34
Proteins 9,729 43,137 29


Functional annotation
General category Metabolism
Detailed category Secondary metabolism

Document:
Function annotation of SCOP domain superfamilies

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 disease0.01602Moderately InformativeInherited
Disease Ontology (DO)skin disease0.01733Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.1153Moderately InformativeInherited
Disease Ontology (DO)periodontal disease0.000274InformativeDirect
Disease Ontology (DO)proteinuria0.00002139Highly InformativeDirect
Disease Ontology (DO)psoriasis0.0007468Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.6209Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.3533Moderately InformativeInherited
Phenotypic Abnormality (PA)Complement deficiency0.00000002682InformativeDirect
Phenotypic Abnormality (PA)CNS infection0.0002978InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)immune system phenotype0.00817Least InformativeInherited
Mammalian Phenotype (MP)mortality/aging0.0679Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.1082Least InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.001787Moderately InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.009194Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.01537Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.1021Moderately InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.2995Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.524Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.6268Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.7521Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal liver physiology0.0009094InformativeDirect
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.001789InformativeInherited
Mammalian Phenotype (MP)abnormal phagocyte morphology0.0107InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.03242InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.09054InformativeInherited
Mammalian Phenotype (MP)abnormal neutrophil morphology0.0005421Highly InformativeDirect
Mammalian Phenotype (MP)abnormal trophoblast layer morphology0.0005638Highly InformativeDirect
Mammalian Phenotype (MP)abnormal pregnancy0.0005774Highly InformativeDirect
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.0006315Highly InformativeDirect
Mammalian Phenotype (MP)abnormal placenta labyrinth morphology0.0008652Highly InformativeDirect
Mammalian Phenotype (MP)abnormal granulocyte number0.002419Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.008522Least InformativeInherited
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.6158Least InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.138Moderately InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.5138Moderately InformativeInherited
Xenopus ANatomical entity (XAN)hindgut0.00001064Highly 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)filament0.0001704Highly 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 transferases0.00000000002142InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Diphosphoric monoester hydrolases0.000000001003Highly InformativeDirect
Enzyme Commission (EC)Intramolecular lyases1Highly InformativeInherited

Document: EC 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 · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]