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Acyl-CoA dehydrogenase NM domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   Acyl-CoA dehydrogenase NM domain-like [ 56644]
Superfamily:   Acyl-CoA dehydrogenase NM domain-like [ 56645] (2)
Families:   Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains [ 56646] (9)
  acyl-CoA oxidase N-terminal domains [ 75600] (2)


Superfamily statistics
Genomes (2,166) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 25,850 113,743 21
Proteins 25,494 112,812 21


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0000004454 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.1231 Least Informative Inherited
Biological Process (BP) lipid metabolic process 0 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.0712 Moderately Informative Inherited
Biological Process (BP) fatty acid metabolic process 0 Informative Direct
Biological Process (BP) lipid catabolic process 0 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0 Informative Direct
Biological Process (BP) fatty acid catabolic process 0 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.00000004078 Highly Informative Direct
Biological Process (BP) lipid modification 0 Highly Informative Direct
Biological Process (BP) icosanoid metabolic process 0.03691 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.000000008296 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0000001924 Moderately Informative Direct
Molecular Function (MF) coenzyme binding 0 Informative Direct
Molecular Function (MF) sulfur compound binding 0.0005486 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000000009568 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.00000000001415 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.995 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.007676 Moderately Informative Inherited
Cellular Component (CC) external encapsulating structure 0.0001482 Informative Direct
Cellular Component (CC) microbody 0 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on the CH-CH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or red0.1185Moderately InformativeInherited
Enzyme Commission (EC)With other acceptors0InformativeDirect
Enzyme Commission (EC)With reduced flavin or flavoprotein as one donor, 0.000000000002343Highly InformativeDirect
Enzyme Commission (EC)With oxygen as acceptor0.0000000003663Highly InformativeDirect
Enzyme Commission (EC)With a flavin as acceptor0.00000001767Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the musculature0.0157Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.07338Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.08651Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.1574Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system physiology0.004145Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of muscle physiology0.005282Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.005812Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of carbohydrate metabolism/homeostasis0.05328Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.07065Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.1926Moderately InformativeInherited
Phenotypic Abnormality (PA)Aciduria0.000001466InformativeDirect
Phenotypic Abnormality (PA)Hypoglycemia0.00001135InformativeDirect
Phenotypic Abnormality (PA)Muscular hypotonia0.0002822InformativeDirect
Phenotypic Abnormality (PA)Abnormality of mitochondrial metabolism0.0006182InformativeDirect
Phenotypic Abnormality (PA)Abnormality of lipid metabolism0.025InformativeInherited
Phenotypic Abnormality (PA)Dicarboxylic aciduria0.000000005036Highly InformativeDirect
Phenotypic Abnormality (PA)Decreased plasma carnitine0.0000002669Highly InformativeDirect
Phenotypic Abnormality (PA)Hepatic steatosis0.00002029Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0.006462Least InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.0006164Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal adaptive thermogenesis0.00000007588InformativeDirect
Mammalian Phenotype (MP)abnormal amino acid level0.000004352InformativeDirect
Mammalian Phenotype (MP)abnormal circulating carnitine level0.00000000000003473Highly InformativeDirect
Mammalian Phenotype (MP)hepatic steatosis0.0000000246Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.00001187Least InformativeDirect
Worm Phenotype (WP)level of transgene expression variant0.01984Moderately InformativeInherited
Worm Phenotype (WP)transgene expression increased0.0003282InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.002051Moderately InformativeInherited
Xenopus ANatomical entity (XAN)skeletal muscle0.000005905InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)pollen tube cell0.00002465InformativeDirect
Plant structure DEvelopment stage (PDE)pollen development stage0.0003585Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)L mature pollen stage0.00007757InformativeDirect
Plant structure DEvelopment stage (PDE)M germinated pollen stage0.0002413InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate0.03361InformativeInherited
Enzyme Commission (EC)Acting on CH or CH(2) groups0.6367InformativeInherited
Enzyme Commission (EC)With oxygen as acceptor0.000000001812Highly InformativeDirect
Enzyme Commission (EC)With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen0.00002653Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0Moderately InformativeDirect
Biological processVirulence0.0002132Moderately InformativeDirect
Biological processAromatic hydrocarbons catabolism0InformativeDirect
Biological processFatty acid metabolism0InformativeDirect
Biological processSteroid metabolism0.2264InformativeInherited
Biological processCholesterol metabolism0.00000003127Highly InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentPeroxisome0InformativeDirect
DiseaseDisease mutation0.0000008428Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionFlavoprotein0Moderately InformativeDirect
Molecular functionFAD0InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationPhosphoprotein0.0000002189Least InformativeDirect
Post-translational modificationS-nitrosylation0.000005005InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)lipid metabolism0Least InformativeDirect
UniPathway (UP)aromatic compound metabolism0.883Least InformativeInherited
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)fatty acid metabolism0Moderately InformativeDirect
UniPathway (UP)amino-acid degradation0.000002544Moderately InformativeDirect
UniPathway (UP)amine and polyamine metabolism0.0001073Moderately InformativeDirect
UniPathway (UP)Branched-chain amino-acid degradation0InformativeDirect
UniPathway (UP)fatty acid degradation4.598e-16InformativeDirect
UniPathway (UP)carnitine metabolism0.00000000000005134InformativeDirect
UniPathway (UP)siderophore metabolism0.0000002966InformativeDirect
UniPathway (UP)steroid metabolism0.001375InformativeInherited
UniPathway (UP)4-hydroxyphenylacetate degradation0.000000000000002272Highly InformativeDirect
UniPathway (UP)cholesterol degradation0.00000000000005436Highly InformativeDirect
UniPathway (UP)fatty acid beta-oxidation1Highly InformativeInherited

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR009100 SSF56645 Protein matches
Abstract

Acyl-CoA dehydrogenases are a family of flavoproteins that catalyse the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with the concomitant reduction of enzyme-bound FAD. Different family members share a high sequence identity, catalytic mechanisms, and structural properties, but differ in the position of their catalytic bases and in their substrate binding specificity. Butyryl-CoA dehydrogenase [PubMed11812788] prefers short chain substrates, medium chain- and long-chain acyl-CoA dehydrogenases prefer medium and long chain substrates, respectively, and Isovaleryl-CoA dehydrogenase [PubMed9214289] prefers branched-chain substrates.

The monomeric enzyme is folded into three domains of approximately equal size, where the N-terminal domain is all-alpha, the middle domain is an open (5,8) barrel, and the C-terminal domain is a four-helical bundle. The constituent families differ in the numbers of C-terminal domains. This entry represents both the N-terminal and middle domains found in medium chain acyl-CoA dehydrogenases, as well as in the related peroxisomal acyl-CoA oxidase-II enzymes. Acyl-CoA oxidase (ACO) catalyzes the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids [PubMed11872165].


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-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · 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 14 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 Acyl-CoA dehydrogenase NM domain-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 14 hidden Markov models representing the Acyl-CoA dehydrogenase NM domain-like 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-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]