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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 (2,680) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 11,591 48,817 11
Proteins 10,459 46,231 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)organonitrogen compound metabolic process0.00000000000010850Least InformativeDirect
Biological Process (BP)biological regulation0.72371Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)primary metabolic process0.000033880.002963Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.053951Least InformativeInherited
Biological Process (BP)biosynthetic process0.23550.7854Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.017581Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)organophosphate biosynthetic process00Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.0000000000000016250.000000000000007296Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.00000000000001350.0000000000001725Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process0.0000000053590.00000000413Moderately InformativeDirect
Biological Process (BP)regulation of macromolecule biosynthetic process0.26071Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process0.34971Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.49961Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.26661Moderately InformativeInherited
Biological Process (BP)regulation of molecular function0.46780.725Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process11Moderately InformativeInherited
Biological Process (BP)regulation of signaling0.0004370.01806Moderately InformativeInherited
Biological Process (BP)regulation of cell communication0.00058740.01739Moderately InformativeInherited
Biological Process (BP)regulation of response to stimulus0.0046180.0302Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.82510.6281Moderately InformativeInherited
Biological Process (BP)gene expression11Moderately InformativeInherited
Biological Process (BP)RNA metabolic process11Moderately InformativeInherited
Biological Process (BP)coenzyme biosynthetic process00InformativeDirect
Biological Process (BP)tRNA metabolic process0.000000000010790.0000000212InformativeDirect
Biological Process (BP)ncRNA processing0.00000000054820.0000005003InformativeDirect
Biological Process (BP)peptidyl-amino acid modification0.002840.0002242InformativeInherited
Biological Process (BP)regulation of immune response0.41870.2113InformativeInherited
Biological Process (BP)positive regulation of immune system process0.063950.03789InformativeInherited
Biological Process (BP)positive regulation of signal transduction0.83160.7729InformativeInherited
Biological Process (BP)regulation of defense response0.60840.07816InformativeInherited
Biological Process (BP)RNA modification0.0054170.004003InformativeInherited
Biological Process (BP)protein modification by small protein conjugation00Highly InformativeDirect
Biological Process (BP)Mo-molybdopterin cofactor metabolic process00Highly InformativeDirect
Biological Process (BP)tRNA modification0.000000000000042880.000000000001048Highly InformativeDirect
Biological Process (BP)regulation of toll-like receptor signaling pathway0.0001660.00000006493Highly InformativeDirect
Biological Process (BP)positive regulation of sequence-specific DNA binding transcription factor activity0.0002450.00005603Highly InformativeDirect
Molecular Function (MF)binding0.48631Least InformativeInherited
Molecular Function (MF)transferase activity0.13481Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.082491Moderately InformativeInherited
Molecular Function (MF)ligase activity00InformativeDirect
Molecular Function (MF)transferase activity, transferring sulfur-containing groups00InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.0000000000000027270.00000000005172InformativeDirect
Molecular Function (MF)protein dimerization activity0.14480.1593InformativeInherited
Molecular Function (MF)enzyme binding0.016050.01599InformativeInherited
Molecular Function (MF)sulfurtransferase activity0.0000000018270.00000000006491Highly InformativeDirect
Molecular Function (MF)protein heterodimerization activity0.0000021510.0004609Highly InformativeDirect
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.14050.05724Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.93570.6139Least InformativeInherited
Cellular Component (CC)nuclear part0.00010760.000255Moderately 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) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.002963 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.7854 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.000000000000007296 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0000000000001725 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00000000413 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.725 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.7549 Moderately Informative Inherited
Biological Process (BP) reproduction 0.1166 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.2704 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.4948 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.01806 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.01739 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.0302 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.6281 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.07353 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0 Informative Direct
Biological Process (BP) tRNA metabolic process 0.0000000212 Informative Direct
Biological Process (BP) ncRNA processing 0.0000005003 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.0002242 Informative Direct
Biological Process (BP) post-embryonic development 0.00004968 Informative Direct
Biological Process (BP) multicellular organism reproduction 0.01909 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.03471 Informative Inherited
Biological Process (BP) single organism reproductive process 0.04021 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.07596 Informative Inherited
Biological Process (BP) regulation of immune response 0.2113 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.725 Informative Inherited
Biological Process (BP) cell death 0.02798 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.03789 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.7729 Informative Inherited
Biological Process (BP) regulation of defense response 0.07816 Informative Inherited
Biological Process (BP) proteolysis 1 Informative Inherited
Biological Process (BP) cell development 0.1007 Informative Inherited
Biological Process (BP) regulation of catabolic process 0.01122 Informative Inherited
Biological Process (BP) RNA modification 0.004003 Informative Inherited
Biological Process (BP) organelle assembly 0.07505 Informative Inherited
Biological Process (BP) protein modification by small protein conjugation 0 Highly Informative Direct
Biological Process (BP) Mo-molybdopterin cofactor metabolic process 0 Highly Informative Direct
Biological Process (BP) tRNA modification 0.000000000001048 Highly Informative Direct
Biological Process (BP) regulation of toll-like receptor signaling pathway 0.00000006493 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 0.00005603 Highly Informative Direct
Biological Process (BP) modification-dependent macromolecule catabolic process 0.00000067 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.00001864 Highly Informative Direct
Biological Process (BP) autophagy 0.00000000000579 Highly Informative Direct
Biological Process (BP) programmed cell death involved in cell development 0.000002145 Highly Informative Direct
Biological Process (BP) positive regulation of cellular catabolic process 0.0008701 Highly Informative Direct
Biological Process (BP) cellular protein catabolic process 0.9588 Highly Informative Inherited
Biological Process (BP) germ cell development 0.001919 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.02785 Highly Informative Inherited
Biological Process (BP) post-embryonic animal morphogenesis 0.006035 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) transferase activity, transferring sulfur-containing groups 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.00000000005172 Informative Direct
Molecular Function (MF) protein dimerization activity 0.1593 Informative Inherited
Molecular Function (MF) enzyme binding 0.01599 Informative Inherited
Molecular Function (MF) sulfurtransferase activity 0.00000000006491 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0004609 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.05724 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.6139 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000255 Moderately Informative Direct

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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.3804Least InformativeInherited
Biological processProtein transport0Moderately InformativeDirect
Biological processUbl conjugation pathway0Moderately InformativeDirect
Biological processAutophagy0InformativeDirect
Biological processtRNA processing0InformativeDirect
Biological processMolybdenum cofactor biosynthesis0Highly InformativeDirect
Cellular componentNucleus0.000000004151Least InformativeDirect
Cellular componentCytoplasm0.000000375Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMetal-binding0.0000002182Least InformativeDirect
Post-translational modificationTransferase0.0001465Least InformativeDirect
Post-translational modificationAcetylation0.0000000002139Least InformativeDirect
Post-translational modificationPhosphoprotein0.0003325Least InformativeDirect
Post-translational modificationUbl conjugation0.0000007394Moderately InformativeDirect

Document: KW 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) · UniProtKB KeyWords (KW) ]

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) · UniProtKB KeyWords (KW) · Internal database links ]