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 (2,106)	Uniprot 2013_05	PDB chains (SCOP 1.75)
Domains	9,709	19,448	11
Proteins	8,735	18,671	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 term	FDR (singleton)	FDR (all)	SDFO level	Annotation (direct or inherited)
Biological Process (BP)	protein metabolic process	0	0	Least Informative	Direct
Biological Process (BP)	cellular macromolecule metabolic process	0	0	Least Informative	Direct
Biological Process (BP)	regulation of metabolic process	0.782	1	Least Informative	Inherited
Biological Process (BP)	regulation of cellular process	0.7239	1	Least Informative	Inherited
Biological Process (BP)	biosynthetic process	0.08222	0.7764	Least Informative	Inherited
Biological Process (BP)	heterocycle metabolic process	0.01033	1	Least Informative	Inherited
Biological Process (BP)	nitrogen compound metabolic process	0.068	1	Least Informative	Inherited
Biological Process (BP)	organic cyclic compound metabolic process	0.04706	1	Least Informative	Inherited
Biological Process (BP)	cellular aromatic compound metabolic process	1	1	Least Informative	Inherited
Biological Process (BP)	phosphate-containing compound metabolic process	9.331e-12	4.463e-07	Moderately Informative	Direct
Biological Process (BP)	heterocycle biosynthetic process	0	3.1e-13	Moderately Informative	Direct
Biological Process (BP)	organophosphate metabolic process	3.11e-08	8.505e-06	Moderately Informative	Direct
Biological Process (BP)	cofactor metabolic process	6.09e-15	1.352e-13	Moderately Informative	Direct
Biological Process (BP)	organic cyclic compound biosynthetic process	4.632e-15	9.609e-12	Moderately Informative	Direct
Biological Process (BP)	organonitrogen compound biosynthetic process	0	7.835e-15	Moderately Informative	Direct
Biological Process (BP)	regulation of biosynthetic process	0.1797	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of gene expression	0.2127	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of cellular metabolic process	0.6308	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of nitrogen compound metabolic process	0.2078	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of molecular function	0.3891	0.4461	Moderately Informative	Inherited
Biological Process (BP)	cellular protein modification process	0.7595	0.4114	Moderately Informative	Inherited
Biological Process (BP)	gene expression	1	1	Moderately Informative	Inherited
Biological Process (BP)	RNA metabolic process	1	1	Moderately Informative	Inherited
Biological Process (BP)	tRNA metabolic process	6.631e-11	6.536e-08	Informative	Direct
Biological Process (BP)	coenzyme biosynthetic process	0	0	Informative	Direct
Biological Process (BP)	ncRNA processing	1.831e-08	5.239e-06	Informative	Direct
Biological Process (BP)	protein modification by small protein conjugation or removal	0	0	Informative	Direct
Biological Process (BP)	peptidyl-amino acid modification	0.9729	1	Informative	Inherited
Biological Process (BP)	RNA modification	0.01374	0.01546	Informative	Inherited
Biological Process (BP)	tRNA modification	1.848e-12	3.826e-11	Highly Informative	Direct
Biological Process (BP)	Mo-molybdopterin cofactor metabolic process	0	0	Highly Informative	Direct
Biological Process (BP)	molybdopterin cofactor biosynthetic process	0	0	Highly Informative	Direct
Biological Process (BP)	positive regulation of sequence-specific DNA binding transcription factor activity	0.0006764	3.571e-05	Highly Informative	Direct
Molecular Function (MF)	transferase activity	0.2065	1	Least Informative	Inherited
Molecular Function (MF)	binding	0.7409	1	Least Informative	Inherited
Molecular Function (MF)	transferase activity, transferring phosphorus-containing groups	0.6554	1	Moderately Informative	Inherited
Molecular Function (MF)	protein binding	0.004002	0.2554	Moderately Informative	Inherited
Molecular Function (MF)	nucleotidyltransferase activity	1.801e-09	2.066e-07	Informative	Direct
Molecular Function (MF)	protein dimerization activity	0.08435	0.04049	Informative	Inherited
Molecular Function (MF)	sulfurtransferase activity	5.216e-11	1.619e-13	Highly Informative	Direct
Molecular Function (MF)	protein heterodimerization activity	2.678e-07	0.0003523	Highly Informative	Direct
Cellular Component (CC)	intracellular membrane-bounded organelle	0.9172	1	Least Informative	Inherited
Cellular Component (CC)	protein complex	0.569	0.9366	Least Informative	Inherited
Cellular Component (CC)	intracellular organelle part	1	1	Least Informative	Inherited
Cellular Component (CC)	cytoplasmic part	0.7386	0.2787	Least Informative	Inherited
Cellular Component (CC)	cytosol	9.6e-08	7.812e-10	Moderately Informative	Direct
Cellular Component (CC)	nuclear part	0.05554	0.4276	Moderately Informative	Inherited

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)	protein metabolic process	0	Least Informative	Direct
Biological Process (BP)	cellular macromolecule metabolic process	0	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)	biosynthetic process	0.7764	Least Informative	Inherited
Biological Process (BP)	heterocycle metabolic process	1	Least Informative	Inherited
Biological Process (BP)	response to stimulus	1	Least Informative	Inherited
Biological Process (BP)	nitrogen compound metabolic process	1	Least Informative	Inherited
Biological Process (BP)	organic cyclic compound metabolic process	1	Least Informative	Inherited
Biological Process (BP)	cellular aromatic compound metabolic process	1	Least Informative	Inherited
Biological Process (BP)	multicellular organismal process	1	Least Informative	Inherited
Biological Process (BP)	developmental process	1	Least Informative	Inherited
Biological Process (BP)	phosphate-containing compound metabolic process	4.463e-07	Moderately Informative	Direct
Biological Process (BP)	heterocycle biosynthetic process	3.1e-13	Moderately Informative	Direct
Biological Process (BP)	organophosphate metabolic process	8.505e-06	Moderately Informative	Direct
Biological Process (BP)	cofactor metabolic process	1.352e-13	Moderately Informative	Direct
Biological Process (BP)	organic cyclic compound biosynthetic process	9.609e-12	Moderately Informative	Direct
Biological Process (BP)	organonitrogen compound biosynthetic process	7.835e-15	Moderately Informative	Direct
Biological Process (BP)	regulation of cellular metabolic process	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of biosynthetic process	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of gene expression	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of nitrogen compound metabolic process	1	Moderately Informative	Inherited
Biological Process (BP)	regulation of molecular function	0.4461	Moderately Informative	Inherited
Biological Process (BP)	organic substance catabolic process	1	Moderately Informative	Inherited
Biological Process (BP)	cellular catabolic process	0.7303	Moderately Informative	Inherited
Biological Process (BP)	cellular protein modification process	0.4114	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)	tRNA metabolic process	6.536e-08	Informative	Direct
Biological Process (BP)	coenzyme biosynthetic process	0	Informative	Direct
Biological Process (BP)	ncRNA processing	5.239e-06	Informative	Direct
Biological Process (BP)	protein modification by small protein conjugation or removal	0	Informative	Direct
Biological Process (BP)	cellular macromolecule catabolic process	0.9282	Informative	Inherited
Biological Process (BP)	proteolysis	1	Informative	Inherited
Biological Process (BP)	protein catabolic process	0.4911	Informative	Inherited
Biological Process (BP)	peptidyl-amino acid modification	1	Informative	Inherited
Biological Process (BP)	response to external stimulus	0.2439	Informative	Inherited
Biological Process (BP)	RNA modification	0.01546	Informative	Inherited
Biological Process (BP)	tRNA modification	3.826e-11	Highly Informative	Direct
Biological Process (BP)	autophagy	1.308e-10	Highly Informative	Direct
Biological Process (BP)	post-embryonic development	7.35e-05	Highly Informative	Direct
Biological Process (BP)	Mo-molybdopterin cofactor metabolic process	0	Highly Informative	Direct
Biological Process (BP)	modification-dependent protein catabolic process	3.971e-05	Highly Informative	Direct
Biological Process (BP)	molybdopterin cofactor biosynthetic process	0	Highly Informative	Direct
Biological Process (BP)	positive regulation of sequence-specific DNA binding transcription factor activity	3.571e-05	Highly Informative	Direct
Molecular Function (MF)	transferase activity	1	Least Informative	Inherited
Molecular Function (MF)	binding	1	Least Informative	Inherited
Molecular Function (MF)	transferase activity, transferring phosphorus-containing groups	1	Moderately Informative	Inherited
Molecular Function (MF)	protein binding	0.2554	Moderately Informative	Inherited
Molecular Function (MF)	nucleotidyltransferase activity	2.066e-07	Informative	Direct
Molecular Function (MF)	protein dimerization activity	0.04049	Informative	Inherited
Molecular Function (MF)	sulfurtransferase activity	1.619e-13	Highly Informative	Direct
Molecular Function (MF)	protein heterodimerization activity	0.0003523	Highly Informative	Direct
Cellular Component (CC)	intracellular membrane-bounded organelle	1	Least Informative	Inherited
Cellular Component (CC)	protein complex	0.9366	Least Informative	Inherited
Cellular Component (CC)	intracellular organelle part	1	Least Informative	Inherited
Cellular Component (CC)	cytoplasmic part	0.2787	Least Informative	Inherited
Cellular Component (CC)	cytosol	7.812e-10	Moderately Informative	Direct
Cellular Component (CC)	nuclear part	0.4276	Moderately Informative	Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Nucleotidyltransferases	0	Least Informative	Direct
Enzyme Commission (EC)	Sulfurtransferases	0	Informative	Direct

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)

	WP term	FDR (all)	SDWP level	Annotation (direct or inherited)
Worm Phenotype (WP)	growth variant	0	Least Informative	Direct
Worm Phenotype (WP)	cell physiology variant	5.257e-05	Least Informative	Direct
Worm Phenotype (WP)	organism metabolism processing variant	0.009157	Least Informative	Inherited
Worm Phenotype (WP)	protein aggregation variant	9.818e-06	Moderately Informative	Direct
Worm Phenotype (WP)	pattern of transgene expression variant	0.0001747	Moderately Informative	Direct
Worm Phenotype (WP)	gametogenesis variant	0.0004242	Moderately Informative	Direct
Worm Phenotype (WP)	meiotic chromosome organization variant	8.996e-05	Informative	Direct
Worm Phenotype (WP)	brood size variant	0.0004109	Informative	Direct

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)

	FP term	FDR (all)	SDFP level	Annotation (direct or inherited)
Fly Phenotype (FP)	cell death defective	0	Informative	Direct
Fly Phenotype (FP)	cell lethal	6.82e-06	Highly Informative	Direct

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)

	FA term	FDR (all)	SDFA level	Annotation (direct or inherited)
Fly Anatomy (FA)	larva	0	Least Informative	Direct
Fly Anatomy (FA)	multi-tissue structure	0	Least Informative	Direct

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)

	XA term	FDR (all)	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	embryo	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	alimentary system	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	male genitalia	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	central nervous system	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	head	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	viscus	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	portion of tissue	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	gonad	0	Least Informative	Direct
Xenopus ANatomical entity (XAN)	ectoderm	0	Moderately Informative	Direct
Xenopus ANatomical entity (XAN)	immune system	0	Moderately Informative	Direct

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)

	AP term	FDR (all)	SDAP level	Annotation (direct or inherited)
Plant structure DEvelopment stage (PDE)	E expanded cotyledon stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	F mature embryo stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	C globular stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	D bilateral stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.04 four leaves visible stage	0	Least Informative	Direct

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)

	EC term	FDR (all)	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Transferring phosphorous-containing groups	0	Least Informative	Direct
Enzyme Commission (EC)	Nucleotidyltransferases	0	Moderately Informative	Direct
Enzyme Commission (EC)	Sulfurtransferases	0	Highly Informative	Direct

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)

	KW term	FDR (all)	SDKW level	Annotation (direct or inherited)
Biological process	Transport	0.3649	Least Informative	Inherited
Biological process	Protein transport	0	Moderately Informative	Direct
Biological process	tRNA processing	0	Informative	Direct
Biological process	Ubl conjugation pathway	0	Informative	Direct
Biological process	Autophagy	0	Highly Informative	Direct
Biological process	Molybdenum cofactor biosynthesis	0	Highly Informative	Direct
Cellular component	Nucleus	4.455e-06	Least Informative	Direct
Cellular component	Cytoplasm	0.000126	Least Informative	Direct
Molecular function	Metal-binding	0	Least Informative	Direct
Molecular function	Nucleotide-binding	0	Least Informative	Direct
Molecular function	Zinc	0	Least Informative	Direct
Post-translational modification	Transferase	3.237e-05	Least Informative	Direct
Post-translational modification	Ligase	4.42e-16	Moderately Informative	Direct
Post-translational modification	Phosphoprotein	1.994e-05	Least Informative	Direct
Post-translational modification	Ubl conjugation	2.303e-05	Moderately Informative	Direct

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)

	UP term	FDR (all)	SDUP level	Annotation (direct or inherited)
UniPathway (UP)	biopolymer metabolism	0	Least Informative	Direct
UniPathway (UP)	cofactor metabolism	3.232e-08	Least Informative	Direct
UniPathway (UP)	tRNA modification	0	Informative	Direct
UniPathway (UP)	molybdopterin biosynthesis	0	Highly Informative	Direct
UniPathway (UP)	protein sumoylation	0	Highly Informative	Direct
UniPathway (UP)	5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis	1.319e-09	Highly Informative	Direct

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 [ PubMed 11713534]. 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) · 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.

SEARCH

BROWSE

TOOLS

ABOUT

HELP

Activating enzymes of the ubiquitin-like proteins superfamily