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Amyloid beta a4 protein copper binding domain (domain 2) superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Dodecin subunit-like [ 88797] (6)
Superfamily:   Amyloid beta a4 protein copper binding domain (domain 2) [ 89811]
Families:   Amyloid beta a4 protein copper binding domain (domain 2) [ 89812]


Superfamily statistics
Genomes (126) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 387 972 1
Proteins 387 970 1


Functional annotation
General category General
Detailed category Ion binding

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) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00000006322 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00002709 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00003066 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.00003539 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.000104 Least Informative Direct
Biological Process (BP) biological regulation 0.0001605 Least Informative Direct
Biological Process (BP) primary metabolic process 0.007754 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.005935 Least Informative Inherited
Biological Process (BP) response to stimulus 0.02504 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.1711 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.01912 Least Informative Inherited
Biological Process (BP) cell differentiation 0.000000003145 Moderately Informative Direct
Biological Process (BP) regulation of signaling 0.00000004733 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.00000008026 Moderately Informative Direct
Biological Process (BP) single-organism transport 0.00000008359 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 0.0000002417 Moderately Informative Direct
Biological Process (BP) reproduction 0.0000002892 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.0000005546 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.000000583 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.0000007408 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0000008208 Moderately Informative Direct
Biological Process (BP) gene expression 0.00000157 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.000002063 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.00000301 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.000005494 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.00001108 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.00001148 Moderately Informative Direct
Biological Process (BP) cellular localization 0.00005473 Moderately Informative Direct
Biological Process (BP) cell communication 0.0000782 Moderately Informative Direct
Biological Process (BP) response to external stimulus 0.0002249 Moderately Informative Direct
Biological Process (BP) tissue development 0.1193 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.3279 Moderately Informative Inherited
Biological Process (BP) single organism signaling 0.00717 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.005549 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.08057 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.02277 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.04771 Moderately Informative Inherited
Biological Process (BP) growth 0 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.000000000000007296 Informative Direct
Biological Process (BP) generation of neurons 0.00000000000001422 Informative Direct
Biological Process (BP) cellular chemical homeostasis 0.00000000000001422 Informative Direct
Biological Process (BP) cation homeostasis 0.00000000000001763 Informative Direct
Biological Process (BP) inorganic ion homeostasis 0.00000000000002102 Informative Direct
Biological Process (BP) regulation of transferase activity 0.00000000000008578 Informative Direct
Biological Process (BP) behavior 0.0000000000002588 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.000000000006121 Informative Direct
Biological Process (BP) epithelium development 0.00000000001482 Informative Direct
Biological Process (BP) microtubule-based process 0.00000000002294 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0000000001577 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.0000000002088 Informative Direct
Biological Process (BP) phosphorylation 0.000000002951 Informative Direct
Biological Process (BP) central nervous system development 0.0000000125 Informative Direct
Biological Process (BP) single-organism cellular localization 0.00000008842 Informative Direct
Biological Process (BP) regulation of growth 0.0000001245 Informative Direct
Biological Process (BP) locomotion 0.000000164 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.0000002134 Informative Direct
Biological Process (BP) regulation of nervous system development 0.0000007161 Informative Direct
Biological Process (BP) regulation of cell cycle 0.000002184 Informative Direct
Biological Process (BP) intracellular transport 0.000003115 Informative Direct
Biological Process (BP) movement of cell or subcellular component 0.00002576 Informative Direct
Biological Process (BP) response to radiation 0.00003496 Informative Direct
Biological Process (BP) circulatory system development 0.0001893 Informative Direct
Biological Process (BP) system process 0.0002614 Informative Direct
Biological Process (BP) multicellular organism reproduction 0.0006182 Informative Direct
Biological Process (BP) regulation of protein modification process 0.02073 Informative Inherited
Biological Process (BP) cell development 0.003606 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.2124 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.01445 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 0.002338 Informative Inherited
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0 Highly Informative Direct
Biological Process (BP) neuron development 0 Highly Informative Direct
Biological Process (BP) cell growth 0 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 0 Highly Informative Direct
Biological Process (BP) plasma membrane bounded cell projection organization 0 Highly Informative Direct
Biological Process (BP) mRNA processing 0 Highly Informative Direct
Biological Process (BP) positive regulation of mitotic cell cycle 0 Highly Informative Direct
Biological Process (BP) morphogenesis of an epithelium 0.00000000000001079 Highly Informative Direct
Biological Process (BP) nervous system process 0.00000000000001763 Highly Informative Direct
Biological Process (BP) anatomical structure maturation 0.00000000000946 Highly Informative Direct
Biological Process (BP) developmental growth involved in morphogenesis 0.00000000006671 Highly Informative Direct
Biological Process (BP) single-organism behavior 0.0000000001133 Highly Informative Direct
Biological Process (BP) cell maturation 0.0000000003284 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.0000001673 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 0.000004462 Highly Informative Direct
Biological Process (BP) locomotory behavior 0.00000653 Highly Informative Direct
Molecular Function (MF) binding 0.0002129 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.000001876 Moderately Informative Direct
Molecular Function (MF) DNA binding 0.00000001609 Informative Direct
Cellular Component (CC) membrane 0.0001873 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.002567 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.4105 Least Informative Inherited
Cellular Component (CC) intrinsic component of membrane 0.000000001282 Moderately Informative Direct
Cellular Component (CC) cell projection 0.000000003581 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.000000199 Moderately Informative Direct
Cellular Component (CC) vesicle 0.008225 Moderately Informative Inherited
Cellular Component (CC) neuron projection 0.00000000001139 Informative Direct
Cellular Component (CC) Golgi apparatus 0.00000000001376 Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis0Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Biological processEndocytosis0InformativeDirect
Biological processNotch signaling pathway0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
Coding sequence diversityAlternative splicing0.0000000000106Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionZinc0.0000000289Least InformativeDirect
Molecular functionMetal-binding0.00001911Least InformativeDirect
Molecular functionIron0.0000008265Moderately InformativeDirect
Molecular functionCopper0InformativeDirect
Post-translational modificationHeparin-binding0InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationSerine protease inhibitor0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0.00001297Least InformativeDirect
Post-translational modificationIsopeptide bond0.0000007044Moderately InformativeDirect
Post-translational modificationUbl conjugation0.00001296Moderately InformativeDirect
Post-translational modificationProteoglycan0.000000000008766InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011178 SSF89811 Protein matches
Abstract

This entry represents a copper-binding domain found within the extracellular domain, which is at the N-terminal of amyloidogenic glycoproteins such as amyloid-beta precursor protein (APP, or A4). The copper-binding domain has a dodecin-like fold consisting of a 2-layer alpha/beta topology [PubMed12611883].

More information about these protein can be found at Protein of the Month: Amyloid-beta Precursor Protein.


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) · 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 1 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 Amyloid beta a4 protein copper binding domain (domain 2) 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 1 hidden Markov models representing the Amyloid beta a4 protein copper binding domain (domain 2) 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) · UniProtKB KeyWords (KW) · Internal database links ]