5JJ4

Crystal Structure of a Variant Human Activation-induced Deoxycytidine Deaminase as an MBP fusion protein

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth C]	SCOP2 Family	APOBEC domain-like	8050542	4005403	SCOP2 (2022-06-29)
A [auth C]	SCOP2 Superfamily	Cytidine deaminase-like	8105530	3001838	SCOP2 (2022-06-29)
B [auth A]	SCOP2B Superfamily	Cytidine deaminase-like	8105530	3001838	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Cytidine deaminase-like	8105530	3001838	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth C]	APOBEC_N	e5jj4C3	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: APOBEC_N	ECOD (1.6)
A [auth C]	SBP_bac_1_C	e5jj4C1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
A [auth C]	SBP_bac_1_N_2	e5jj4C4	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_N_2	ECOD (1.6)
B [auth A]	APOBEC_N	e5jj4A3	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: APOBEC_N	ECOD (1.6)
B [auth A]	SBP_bac_1_C	e5jj4A1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
B [auth A]	SBP_bac_1_N_2	e5jj4A4	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_N_2	ECOD (1.6)
C [auth B]	APOBEC_N	e5jj4B2	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: APOBEC_N	ECOD (1.6)
C [auth B]	SBP_bac_1_C,SBP_bac_1_N_2	e5jj4B3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C,SBP_bac_1_N_2	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B [auth A], C [auth B]	PF01547	Bacterial extracellular solute-binding protein (SBP_bac_1)	Bacterial extracellular solute-binding protein	-	Family
A [auth C], B [auth A], C [auth B]	PF08210	APOBEC-like N-terminal domain (APOBEC_N)	APOBEC-like N-terminal domain	A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More sp ...	A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination.APOBEC-3 like members contain two copies of this domain. RNA editing by APOBEC-1 requires homodimerisation and this complex interacts with RNA binding proteins to from the editosome [1] (and references therein). This family also includes the functionally homologous activation induced deaminase (AID), which is essential for the development of antibody diversity in B lymphocytes, and the sea lamprey PmCDA1 and PmCDA2, which are predicted to play an AID-like role in the adaptive immune response of jawless vertebrates [2]. Divergent members of this family are present in various eukaryotes such as Nematostella, C. elegans, Micromonas and Emiliania, and prokaryotes such as Wolbachia and Pseudomonas brassicacearum [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth A], C [auth B]	Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase	RNA binding binding organic cyclic compound binding nucleic acid binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines cytidine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding RNA binding binding organic cyclic compound binding nucleic acid binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines cytidine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein binding transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity	regulation of cellular process nuclear DNA replication cell cycle DNA replication regulation of primary metabolic process nucleobase-containing compound metabolic process cell cycle regulation of nucleobase-containing compound metabolic process regulation of cell cycle cell cycle process DNA-templated DNA replication regulation of biological process regulation of nuclear cell cycle DNA replication regulation of cell cycle process biological regulation regulation of cellular process nuclear DNA replication cell cycle DNA replication regulation of primary metabolic process nucleobase-containing compound metabolic process cell cycle regulation of nucleobase-containing compound metabolic process regulation of cell cycle cell cycle process DNA-templated DNA replication regulation of biological process regulation of nuclear cell cycle DNA replication regulation of cell cycle process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process DNA replication regulation of DNA-templated DNA replication metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development leukocyte differentiation RNA modification cytidine to uridine editing base conversion or substitution editing macromolecule modification RNA metabolic process cellular response to stimulus biological process involved in interspecies interaction between organisms response to lipid response to stimulus response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin immune system development production of molecular mediator of immune response immunoglobulin production cellular biosynthetic process somatic diversification of immune receptors via somatic mutation cellular metabolic process gene expression macromolecule biosynthetic process somatic diversification of immunoglobulins multicellular organism development biosynthetic process somatic diversification of immune receptors somatic hypermutation of immunoglobulin genes system development nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA processing defense response defense response to bacterium defense response to other organism response to stress positive regulation of biological process positive regulation of cellular metabolic process positive regulation of gene expression via chromosomal CpG island demethylation positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization positive regulation of metabolic process DNA-templated transcription transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process epigenetic regulation of gene expression regulation of cellular metabolic process DNA-templated transcription initiation regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process positive regulation of cellular biosynthetic process DNA deamination DNA modification DNA cytosine deamination glycosyl compound metabolic process catabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process pyrimidine nucleoside metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process cytidine deamination carbohydrate derivative catabolic process pyrimidine-containing compound metabolic process pyrimidine nucleoside catabolic process cytidine metabolic process glycosyl compound catabolic process nucleoside metabolic process nucleobase-containing compound catabolic process cytidine catabolic process pyrimidine ribonucleoside metabolic process nucleobase-containing small molecule catabolic process nucleoside catabolic process pyrimidine ribonucleoside catabolic process small molecule catabolic process ribonucleoside catabolic process ribonucleoside metabolic process negative regulation of biological process viral life cycle negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process negative regulation of metabolic process single stranded viral RNA replication via double stranded DNA intermediate negative regulation of cellular biosynthetic process viral genome replication negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process regulation of single stranded viral RNA replication via double stranded DNA intermediate negative regulation of single stranded viral RNA replication via double stranded DNA intermediate negative regulation of viral process viral RNA genome replication viral process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process negative regulation of viral genome replication regulation of viral process regulation of viral life cycle negative regulation of biosynthetic process regulation of viral genome replication adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity B cell activation involved in immune response cell activation involved in immune response leukocyte mediated immunity somatic recombination of immunoglobulin genes involved in immune response immune response DNA recombination immune effector process B cell mediated immunity isotype switching immunoglobulin production involved in immunoglobulin-mediated immune response somatic cell DNA recombination somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments leukocyte activation involved in immune response lymphocyte activation involved in immune response immunoglobulin mediated immune response adaptive immune response somatic diversification of immune receptors via germline recombination within a single locus defense response to symbiont defense response to virus response to virus	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex cytoplasmic ribonucleoprotein granule ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle supramolecular complex P-body non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex cytoplasmic ribonucleoprotein granule ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle supramolecular complex P-body non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth A], C [auth B]	IPR050610	APOBEC Cytidine Deaminase	Family
A [auth C], B [auth A], C [auth B]	IPR016193	Cytidine deaminase-like	Homologous Superfamily
A [auth C], B [auth A], C [auth B]	IPR013158	APOBEC-like, N-terminal	Domain
A [auth C], B [auth A], C [auth B]	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain
A [auth C], B [auth A], C [auth B]	IPR016192	APOBEC/CMP deaminase, zinc-binding	Binding Site
A [auth C], B [auth A], C [auth B]	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
A [auth C], B [auth A], C [auth B]	IPR006059	Bacterial-type extracellular solute-binding protein	Family
A [auth C], B [auth A], C [auth B]	IPR006061	Solute-binding family 1, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth C], B [auth A], C [auth B]	Pharos: Q9GZX7	autoimmune disease hyper-IgM syndrome type 1 lymphoid leukemia blast phase chronic myelogenous leukemia, BCR-ABL1 positive hyper-IgM syndrome type 2 hyper-IgM syndrome lymphocytic leukemia peripheral neuropathy ovarian cancer psoriasis peripheral nervous system disease Sjogren syndrome

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.