LeuD/IlvD-like superfamily

SCOP classification

Root:	SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:	Alpha and beta proteins (a/b) [ 51349] (147)
Fold:	The "swivelling" beta/beta/alpha domain [ 52008] (10)
Superfamily:	LeuD/IlvD-like [ 52016] (3)
Families:	LeuD-like [ 52017] (4)
	IlvD/EDD C-terminal domain-like [ 141976]
	AF0055-like [ 141979]

Superfamily statistics

	Genomes (2,233)	Uniprot 2013_05	PDB chains (SCOP 1.75)
Domains	9,941	28,827	13
Proteins	9,925	28,817	13

Functional annotation

General category	Metabolism
Detailed category	Energy

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)	biosynthetic process	0.001928	0.04371	Least Informative	Inherited
Biological Process (BP)	nitrogen compound metabolic process	0.004826	0.6384	Least Informative	Inherited
Biological Process (BP)	single-organism metabolic process	0.01507	1.119e-13	Least Informative	Inherited
Biological Process (BP)	cellular amino acid metabolic process	0.0005817	1.2e-06	Moderately Informative	Direct
Biological Process (BP)	organonitrogen compound biosynthetic process	1.792e-08	4.828e-08	Moderately Informative	Direct
Biological Process (BP)	small molecule biosynthetic process	2.204e-05	0.2318	Moderately Informative	Inherited
Biological Process (BP)	alpha-amino acid biosynthetic process	9.115e-08	0.01431	Informative	Inherited
Biological Process (BP)	branched-chain amino acid metabolic process	2.392e-05	4.063e-10	Highly Informative	Direct

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)	single-organism metabolic process	1.119e-13	Least Informative	Direct
Biological Process (BP)	regulation of metabolic process	1	Least Informative	Inherited
Biological Process (BP)	response to stimulus	0.8869	Least Informative	Inherited
Biological Process (BP)	nitrogen compound metabolic process	0.6384	Least Informative	Inherited
Biological Process (BP)	biosynthetic process	0.04371	Least Informative	Inherited
Biological Process (BP)	single-organism cellular process	1	Least Informative	Inherited
Biological Process (BP)	regulation of cellular process	1	Least Informative	Inherited
Biological Process (BP)	cellular amino acid metabolic process	1.2e-06	Moderately Informative	Direct
Biological Process (BP)	organonitrogen compound biosynthetic process	4.828e-08	Moderately Informative	Direct
Biological Process (BP)	carbohydrate metabolic process	0.04548	Moderately Informative	Inherited
Biological Process (BP)	organic substance catabolic process	0.7664	Moderately Informative	Inherited
Biological Process (BP)	small molecule biosynthetic process	0.2318	Moderately Informative	Inherited
Biological Process (BP)	homeostatic process	0.02311	Moderately Informative	Inherited
Biological Process (BP)	regulation of gene expression	0.5873	Moderately Informative	Inherited
Biological Process (BP)	regulation of biosynthetic process	0.5272	Moderately Informative	Inherited
Biological Process (BP)	regulation of cellular metabolic process	0.9066	Moderately Informative	Inherited
Biological Process (BP)	regulation of protein metabolic process	0.01167	Moderately Informative	Inherited
Biological Process (BP)	oxidation-reduction process	0.01155	Moderately Informative	Inherited
Biological Process (BP)	response to inorganic substance	8.227e-08	Informative	Direct
Biological Process (BP)	posttranscriptional regulation of gene expression	1.173e-05	Informative	Direct
Biological Process (BP)	energy derivation by oxidation of organic compounds	0.0004324	Informative	Direct
Biological Process (BP)	carbohydrate catabolic process	0.0009279	Informative	Direct
Biological Process (BP)	alpha-amino acid biosynthetic process	0.01431	Informative	Inherited
Biological Process (BP)	cellular cation homeostasis	0.2723	Informative	Inherited
Biological Process (BP)	metal ion homeostasis	0.6596	Informative	Inherited
Biological Process (BP)	regulation of translation	8.776e-08	Highly Informative	Direct
Biological Process (BP)	aerobic respiration	0	Highly Informative	Direct
Biological Process (BP)	branched-chain amino acid metabolic process	4.063e-10	Highly Informative	Direct
Molecular Function (MF)	binding	0.01518	Least Informative	Inherited
Molecular Function (MF)	lyase activity	0	Moderately Informative	Direct
Molecular Function (MF)	organic cyclic compound binding	6.279e-08	Moderately Informative	Direct
Molecular Function (MF)	heterocyclic compound binding	4.341e-08	Moderately Informative	Direct
Molecular Function (MF)	cation binding	0.001056	Moderately Informative	Inherited
Molecular Function (MF)	RNA binding	4.499e-10	Informative	Direct
Molecular Function (MF)	carbon-oxygen lyase activity	0	Informative	Direct
Molecular Function (MF)	transition metal ion binding	2.289e-05	Informative	Direct
Molecular Function (MF)	metal cluster binding	0	Highly Informative	Direct
Cellular Component (CC)	cytoplasmic part	1.608e-08	Least Informative	Direct
Cellular Component (CC)	intracellular organelle part	1	Least Informative	Inherited
Cellular Component (CC)	intracellular membrane-bounded organelle	0.006582	Least Informative	Inherited
Cellular Component (CC)	mitochondrial part	0.06291	Moderately Informative	Inherited
Cellular Component (CC)	intracellular organelle lumen	0.5532	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)	Lyases	0	Least Informative	Direct
Enzyme Commission (EC)	Hydro-lyases	0	Moderately Informative	Direct
Enzyme Commission (EC)	Aconitate hydratase	0	Highly Informative	Direct
Enzyme Commission (EC)	2-methylisocitrate dehydratase	0.0002439	Highly Informative	Direct

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)

	XA term	FDR (all)	SDXA level	Annotation (direct or inherited)
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)	cell	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)	musculoskeletal system	0	Moderately Informative	Direct
Xenopus ANatomical entity (XAN)	surface structure	0	Moderately Informative	Direct
Xenopus ANatomical entity (XAN)	multi-tissue structure	0	Moderately Informative	Direct
Xenopus ANatomical entity (XAN)	gamete	0	Moderately Informative	Direct
Xenopus ANatomical entity (XAN)	immune system	0	Moderately Informative	Direct
Xenopus ANatomical entity (XAN)	skin	0	Informative	Direct
Xenopus ANatomical entity (XAN)	lung	0	Informative	Direct
Xenopus ANatomical entity (XAN)	endocrine system	0	Informative	Direct
Xenopus ANatomical entity (XAN)	tail	0	Informative	Direct
Xenopus ANatomical entity (XAN)	oviduct	0	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 ANatomical entity (PAN)	shoot apex	0	Least Informative	Direct
Plant ANatomical entity (PAN)	shoot internode	0	Least Informative	Direct
Plant ANatomical entity (PAN)	plant cell	0	Least Informative	Direct
Plant ANatomical entity (PAN)	root	0	Least Informative	Direct
Plant ANatomical entity (PAN)	portion of meristem tissue	0	Least Informative	Direct
Plant ANatomical entity (PAN)	vascular leaf	0	Least Informative	Direct
Plant ANatomical entity (PAN)	megasporophyll	0	Least Informative	Direct
Plant ANatomical entity (PAN)	microsporophyll	0	Least Informative	Direct
Plant ANatomical entity (PAN)	sepal	0	Least Informative	Direct
Plant ANatomical entity (PAN)	petal	0	Least Informative	Direct
Plant ANatomical entity (PAN)	stem	0	Least Informative	Direct
Plant ANatomical entity (PAN)	androecium	0	Least Informative	Direct
Plant ANatomical entity (PAN)	gynoecium	0	Least Informative	Direct
Plant ANatomical entity (PAN)	leaf lamina	0	Least Informative	Direct
Plant ANatomical entity (PAN)	collective leaf structure	0	Least Informative	Direct
Plant ANatomical entity (PAN)	stalk	0	Least Informative	Direct
Plant ANatomical entity (PAN)	phyllome apex	0	Least Informative	Direct
Plant ANatomical entity (PAN)	guard cell	0	Moderately Informative	Direct
Plant structure DEvelopment stage (PDE)	4 leaf senescence stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.12 twelve leaves visible stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.08 eight leaves visible stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.02 two leaves visible stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.10 ten leaves visible stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.04 four leaves visible stage	0	Least Informative	Direct
Plant structure DEvelopment stage (PDE)	LP.06 six 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)	Lyases	0	Least Informative	Direct
Enzyme Commission (EC)	Carbon-oxygen lyases	0	Moderately 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	Amino-acid biosynthesis	0	Moderately Informative	Direct
Biological process	Tricarboxylic acid cycle	0	Informative	Direct
Biological process	Branched-chain amino acid biosynthesis	0	Highly Informative	Direct
Domain	Transit peptide	0.0006375	Moderately Informative	Direct
Molecular function	Metal-binding	0	Least Informative	Direct
Molecular function	Iron	0	Moderately Informative	Direct
Molecular function	4Fe-4S	0	Informative	Direct
Molecular function	Iron-sulfur	0	Informative	Direct
Post-translational modification	Lyase	0	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)	amino-acid metabolism	0	Least Informative	Direct
UniPathway (UP)	carbohydrate metabolism	1	Least Informative	Inherited
UniPathway (UP)	proteinogenic amino-acid biosynthesis	0	Moderately Informative	Direct
UniPathway (UP)	L-isoleucine biosynthesis	0	Informative	Direct
UniPathway (UP)	tricarboxylic acid cycle	5.387e-14	Informative	Direct
UniPathway (UP)	L-lysine biosynthesis	1	Informative	Inherited
UniPathway (UP)	L-lysine biosynthesis via AAA pathway	0	Highly Informative	Direct
UniPathway (UP)	L-leucine biosynthesis	0	Highly Informative	Direct
UniPathway (UP)	L-valine biosynthesis	0	Highly Informative	Direct
UniPathway (UP)	glyoxylate and dicarboxylate metabolism	1.929e-07	Highly Informative	Direct

Document: UP annotation of SCOP domains

InterPro annotation

Cross references IPR015928 SSF52016 Protein matches

Abstract
This entry represents the 'swivel' domain found at the C-terminal of eukaryotic mAcn, cAcn/IPR1 and IRP2, and bacterial AcnA, but in the N-terminal region following the HEAT-like domain in bacterial AcnB. This domain has a three layer beta/beta/alpha structure, and in cytosolic Acn is known to rotate between the cAcn and IRP1 forms of the enzyme. This domain is also found in the small subunit of isopropylmalate dehydratase (LeuD).

More information about these proteins can be found at Protein of the Month: Aconitase.

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) · 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 6 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 LeuD/IlvD-like 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 6 hidden Markov models representing the LeuD/IlvD-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.

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LeuD/IlvD-like superfamily