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Activating enzymes of the ubiquitin-like proteins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Activating enzymes of the ubiquitin-like proteins [ 69571]
Superfamily:   Activating enzymes of the ubiquitin-like proteins [ 69572] (2)
Families:   Molybdenum cofactor biosynthesis protein MoeB [ 69573]
  Ubiquitin activating enzymes (UBA) [ 89763] (2)


Superfamily statistics
Genomes (2,675) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 11,511 40,493 11
Proteins 10,393 39,302 11


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

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)macromolecule metabolic process00Least InformativeDirect
Biological Process (BP)primary metabolic process0.0000017930.0000007639Least InformativeDirect
Biological Process (BP)biosynthetic process0.20390.468Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.039891Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)biological regulation0.58961Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.10570.2194Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.010640.8903Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)cofactor metabolic process0.0000000028040.0000000004741Moderately InformativeDirect
Biological Process (BP)organophosphate biosynthetic process00Moderately InformativeDirect
Biological Process (BP)regulation of biosynthetic process0.32611Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.34981Moderately InformativeInherited
Biological Process (BP)regulation of cellular metabolic process11Moderately InformativeInherited
Biological Process (BP)regulation of nitrogen compound metabolic process0.34061Moderately InformativeInherited
Biological Process (BP)regulation of molecular function0.47660.6655Moderately InformativeInherited
Biological Process (BP)regulation of cell communication0.00082830.02434Moderately InformativeInherited
Biological Process (BP)regulation of response to stimulus0.004270.03609Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process11Moderately InformativeInherited
Biological Process (BP)regulation of signaling0.00040250.02408Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.76660.5422Moderately InformativeInherited
Biological Process (BP)RNA metabolic process11Moderately InformativeInherited
Biological Process (BP)gene expression11Moderately InformativeInherited
Biological Process (BP)tRNA metabolic process0.0000000000051480.000000009446InformativeDirect
Biological Process (BP)coenzyme biosynthetic process00InformativeDirect
Biological Process (BP)ncRNA processing0.00000000030730.0000003311InformativeDirect
Biological Process (BP)regulation of transcription, DNA-templated0.1011InformativeInherited
Biological Process (BP)regulation of defense response0.55120.06975InformativeInherited
Biological Process (BP)positive regulation of immune system process0.059510.02628InformativeInherited
Biological Process (BP)positive regulation of signal transduction0.84050.6996InformativeInherited
Biological Process (BP)regulation of immune response0.43530.1802InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.0012780.0001997InformativeInherited
Biological Process (BP)RNA modification0.0052230.003332InformativeInherited
Biological Process (BP)tRNA modification0.000000000000028070.0000000000007127Highly InformativeDirect
Biological Process (BP)Mo-molybdopterin cofactor metabolic process00Highly InformativeDirect
Biological Process (BP)protein modification by small protein conjugation00Highly InformativeDirect
Biological Process (BP)regulation of toll-like receptor signaling pathway0.00015870.00000002306Highly InformativeDirect
Biological Process (BP)regulation of sequence-specific DNA binding transcription factor activity0.0014380.000339Highly InformativeInherited
Molecular Function (MF)binding0.65041Least InformativeInherited
Molecular Function (MF)transferase activity0.18751Least InformativeInherited
Molecular Function (MF)protein binding0.0019970.2393Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.056821Moderately InformativeInherited
Molecular Function (MF)nucleotidyltransferase activity0.000000000000001370.00000000003548InformativeDirect
Molecular Function (MF)transferase activity, transferring sulfur-containing groups00InformativeDirect
Molecular Function (MF)ligase activity00InformativeDirect
Molecular Function (MF)protein dimerization activity0.068630.05709InformativeInherited
Molecular Function (MF)enzyme binding0.028490.04117InformativeInherited
Molecular Function (MF)sulfurtransferase activity0.000000003390.0000000001124Highly InformativeDirect
Molecular Function (MF)protein heterodimerization activity0.00000058490.0005056Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.46150.455Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.42630.1146Least InformativeInherited
Cellular Component (CC)nuclear part0.038780.1145Moderately 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) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000007639 Least Informative Direct
Biological Process (BP) biosynthetic process 0.468 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.2194 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.8903 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cofactor metabolic process 0.0000000004741 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.6655 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.2456 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.4966 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.3195 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.02434 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.03609 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.02408 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.5422 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) tRNA metabolic process 0.000000009446 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 0 Informative Direct
Biological Process (BP) post-embryonic development 0.0001974 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.0001997 Informative Direct
Biological Process (BP) ncRNA processing 0.0000003311 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 1 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.1266 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.06595 Informative Inherited
Biological Process (BP) single organism reproductive process 0.1178 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.1287 Informative Inherited
Biological Process (BP) cell development 0.1029 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.7357 Informative Inherited
Biological Process (BP) regulation of defense response 0.06975 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.02628 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.6996 Informative Inherited
Biological Process (BP) regulation of immune response 0.1802 Informative Inherited
Biological Process (BP) proteolysis 1 Informative Inherited
Biological Process (BP) RNA modification 0.003332 Informative Inherited
Biological Process (BP) tRNA modification 0.0000000000007127 Highly Informative Direct
Biological Process (BP) autophagy 0.0000000004302 Highly Informative Direct
Biological Process (BP) aging 0.0004017 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.00001484 Highly Informative Direct
Biological Process (BP) Mo-molybdopterin cofactor metabolic process 0 Highly Informative Direct
Biological Process (BP) modification-dependent protein catabolic process 0.000002787 Highly Informative Direct
Biological Process (BP) protein modification by small protein conjugation 0 Highly Informative Direct
Biological Process (BP) regulation of toll-like receptor signaling pathway 0.00000002306 Highly Informative Direct
Biological Process (BP) regulation of sequence-specific DNA binding transcription factor activity 0.000339 Highly Informative Direct
Biological Process (BP) germ cell development 0.004539 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.009406 Highly Informative Inherited
Biological Process (BP) lipoprotein metabolic process 0.001318 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) protein binding 0.2393 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0.00000000003548 Informative Direct
Molecular Function (MF) transferase activity, transferring sulfur-containing groups 0 Informative Direct
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) protein dimerization activity 0.05709 Informative Inherited
Molecular Function (MF) enzyme binding 0.04117 Informative Inherited
Molecular Function (MF) sulfurtransferase activity 0.0000000001124 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0005056 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.455 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1146 Least Informative Inherited
Cellular Component (CC) nuclear part 0.1145 Moderately Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Sulfurtransferases0InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0001086Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0002887Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.0006288Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.001145Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.01195Least InformativeInherited
Worm Phenotype (WP)protein protein interaction variant0.000001626Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.0001517Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.0002224Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0005083Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.06912Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.1542Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.2253Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.2501Moderately InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0.0001397InformativeDirect
Worm Phenotype (WP)protruding vulva0.0001668InformativeDirect
Worm Phenotype (WP)meiotic chromosome organization variant0.0001833InformativeDirect
Worm Phenotype (WP)brood size variant0.001172InformativeInherited
Worm Phenotype (WP)epithelial system development variant0.09804InformativeInherited
Worm Phenotype (WP)exploded through vulva0.0004507Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)cell death defective0InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect
Fly Anatomy (FA)developing material anatomical entity0Moderately InformativeDirect
Fly Anatomy (FA)pupa0InformativeDirect

Document: FA 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)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0Least 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)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases0.0007902Moderately InformativeDirect
Enzyme Commission (EC)Sulfurtransferases0Highly InformativeDirect
Enzyme Commission (EC)Acid--thiol ligases1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.3653Least InformativeInherited
Biological processProtein transport0Moderately InformativeDirect
Biological processUbl conjugation pathway0Moderately InformativeDirect
Biological processAutophagy0InformativeDirect
Biological processtRNA processing0InformativeDirect
Biological processMolybdenum cofactor biosynthesis0Highly InformativeDirect
Cellular componentNucleus0.0000000217Least InformativeDirect
Cellular componentCytoplasm0.000001144Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMetal-binding0.0000000000006704Least InformativeDirect
Molecular functionATP-binding0.000000005137Moderately InformativeDirect
Post-translational modificationTransferase0.00008695Least InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationAcetylation0.0000000002279Least InformativeDirect
Post-translational modificationPhosphoprotein0.0003533Least InformativeDirect
Post-translational modificationUbl conjugation0.0000005611Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)cofactor metabolism0.00000002927Least InformativeDirect
UniPathway (UP)tRNA modification0InformativeDirect
UniPathway (UP)molybdopterin biosynthesis0Highly InformativeDirect
UniPathway (UP)protein sumoylation0Highly InformativeDirect
UniPathway (UP)5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis0.000000001609Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR009036 SSF69572 Protein matches
Abstract

The Escherichia coli protein is involved in molybdenum cofactor (MoCF) biosynthesis, an evolutionarily conserved pathway. MoeB activates the C terminus of MoaD to form an acyl-adenylate, which is subsequently converted to a thiocarboxylate that acts as the sulphur donor during Moco biosynthesis. The structure of MoeB consists of a three-layer sandwich of alpha/beta/alpha [PubMed11713534]. The sandwich is composed of eight beta-strands, which form a continuous mixed beta sheet in the order 32145678 surrounded by eight helices. Beta strands 6 and 8 are antiparallel to the rest. The N-terminal half of the sheet contains the ATP nucleotide-binding site, which is similar to that of the NAD-binding Rossmann fold. A loop between beta-1 and alpha-3 contains a glycine-rich motif similar to the P loop found in enzymes that hydrolyse ATP. The C-terminal half of the sheet contains a fold that is similar to that found in a family of sugar-binding proteins.


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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · 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 3 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 Activating enzymes of the ubiquitin-like proteins 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 3 hidden Markov models representing the Activating enzymes of the ubiquitin-like proteins 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]