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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 (122) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 379 462 1
Proteins 379 461 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) cellular component organization or biogenesis 0.000000002113 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00001656 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00003711 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.00004151 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0001278 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.008505 Least Informative Inherited
Biological Process (BP) biological regulation 0.02049 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.09836 Least Informative Inherited
Biological Process (BP) response to stimulus 0.01232 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.0202 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0.000000005068 Moderately Informative Direct
Biological Process (BP) cellular localization 0.000000007842 Moderately Informative Direct
Biological Process (BP) gene expression 0.00000002856 Moderately Informative Direct
Biological Process (BP) single-organism transport 0.00000005376 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.000000135 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.0000001361 Moderately Informative Direct
Biological Process (BP) reproduction 0.0000001719 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.0000004382 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.000003584 Moderately Informative Direct
Biological Process (BP) signaling 0.000003946 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.000005806 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.000006671 Moderately Informative Direct
Biological Process (BP) regulation of signaling 0.00002599 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 0.00007143 Moderately Informative Direct
Biological Process (BP) cellular developmental process 0.0001488 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.000154 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.0002219 Moderately Informative Direct
Biological Process (BP) response to external stimulus 0.0002334 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.0003344 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0005074 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.03916 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.01413 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.06563 Moderately Informative Inherited
Biological Process (BP) cell communication 0.004338 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.0017 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.0111 Moderately Informative Inherited
Biological Process (BP) system development 0.002461 Moderately Informative Inherited
Biological Process (BP) growth 0 Informative Direct
Biological Process (BP) generation of neurons 0 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.000000000000005508 Informative Direct
Biological Process (BP) cellular chemical homeostasis 0.000000000000007239 Informative Direct
Biological Process (BP) ion homeostasis 0.00000000000002582 Informative Direct
Biological Process (BP) regulation of transferase activity 0.00000000000009902 Informative Direct
Biological Process (BP) behavior 0.0000000000001283 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.000000000007458 Informative Direct
Biological Process (BP) epithelium development 0.0000000002136 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.0000000002164 Informative Direct
Biological Process (BP) microtubule-based process 0.000000001592 Informative Direct
Biological Process (BP) regulation of growth 0.000000001803 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.000000002014 Informative Direct
Biological Process (BP) phosphorylation 0.000000003945 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.000000005384 Informative Direct
Biological Process (BP) regulation of cell cycle 0.00000003479 Informative Direct
Biological Process (BP) locomotion 0.00000005999 Informative Direct
Biological Process (BP) single-organism intracellular transport 0.0000001134 Informative Direct
Biological Process (BP) central nervous system development 0.0000003037 Informative Direct
Biological Process (BP) movement of cell or subcellular component 0.00001617 Informative Direct
Biological Process (BP) response to radiation 0.00002942 Informative Direct
Biological Process (BP) multicellular organism reproduction 0.0002814 Informative Direct
Biological Process (BP) cell development 0.0003835 Informative Direct
Biological Process (BP) circulatory system development 0.0003988 Informative Direct
Biological Process (BP) system process 0.0005993 Informative Direct
Biological Process (BP) regulation of protein modification process 0.02343 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.2155 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 0.002119 Informative Inherited
Biological Process (BP) cell projection organization 0 Highly Informative Direct
Biological Process (BP) neuron development 0 Highly Informative Direct
Biological Process (BP) positive regulation of mitotic cell cycle 0 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 0 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) cell growth 0 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0 Highly Informative Direct
Biological Process (BP) mRNA metabolic process 0.00000000000001068 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 0.00000000000008346 Highly Informative Direct
Biological Process (BP) morphogenesis of an epithelium 0.0000000000004568 Highly Informative Direct
Biological Process (BP) developmental growth involved in morphogenesis 0.0000000000008409 Highly Informative Direct
Biological Process (BP) single-organism behavior 0.00000000005028 Highly Informative Direct
Biological Process (BP) cell maturation 0.0000000006393 Highly Informative Direct
Biological Process (BP) chemotaxis 0.000000004006 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.00000005681 Highly Informative Direct
Biological Process (BP) locomotory behavior 0.000007711 Highly Informative Direct
Molecular Function (MF) binding 0.0001096 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.000000935 Moderately Informative Direct
Molecular Function (MF) DNA binding 0.000000006398 Informative Direct
Cellular Component (CC) membrane 0.000151 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.000355 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.3314 Least Informative Inherited
Cellular Component (CC) intrinsic component of membrane 0.00000000106 Moderately Informative Direct
Cellular Component (CC) cell projection 0.000000002208 Moderately Informative Direct
Cellular Component (CC) vesicle 0.01298 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0.000000000001468 Informative Direct
Cellular Component (CC) neuron projection 0.000000000001678 Informative Direct

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)growth/size/body region phenotype0Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)abnormal body size0Moderately InformativeDirect
Mammalian Phenotype (MP)lethality during fetal growth through weaning0Moderately InformativeDirect
Mammalian Phenotype (MP)decreased body size0InformativeDirect

Document: MP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0Least InformativeDirect
Xenopus ANatomical entity (XAN)brain0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)immune system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)sensory system0Moderately InformativeDirect

Document: XA 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 splicing0.00000000001039Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionZinc0.00000007445Least InformativeDirect
Molecular functionMetal-binding0.00005492Least InformativeDirect
Molecular functionIron0.000001061Moderately InformativeDirect
Molecular functionCopper0InformativeDirect
Molecular functionHeparin-binding0InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationSerine protease inhibitor0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0.00001307Least InformativeDirect
Post-translational modificationIsopeptide bond0.00000004964Moderately InformativeDirect
Post-translational modificationUbl conjugation0.000002503Moderately InformativeDirect
Post-translational modificationProteoglycan0.0000000003612InformativeDirect

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) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · 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) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]