5JJ4 | pdb_00005jj4

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
Domain Annotation: CATH
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)
C [auth B]	SCOP2B Superfamily	Cytidine deaminase-like	8105530	3001838	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Cytidine deaminase-like	8105530	3001838	SCOP2B (2022-06-29)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth B]	EFhand_Ca_insen	e5jj4B2	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: EF-hand-related	T: EF-hand	F: EFhand_Ca_insen	ECOD (v294.1)
C [auth B]	Pro_isomerase	e5jj4B3	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
B [auth A]	FRB_dom	e5jj4A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: FRB_dom	ECOD (v294.1)
B [auth A]	KWL1	e5jj4A4	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: KWL1	ECOD (v294.1)
A [auth C]	FRB_dom	e5jj4C1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: FRB_dom	ECOD (v294.1)
A [auth C]	KWL1	e5jj4C4	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: KWL1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth B]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
C [auth B]	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (utative)
B [auth A]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
B [auth A]	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (utative)
A [auth C]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
A [auth C]	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (utative)

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	Activation-induced cytidine deaminase (AID) (AID)	Activation-induced cytidine deaminase (AID)	This entry represents Activation-induced cytidine deaminase (AID), which is a single-stranded DNA-specific cytidine deaminase. It is involved in somatic hypermutation, gene conversion, and class-switch recombination in B-lymphocytes by deaminating C ...	This entry represents Activation-induced cytidine deaminase (AID), which is a single-stranded DNA-specific cytidine deaminase. It is involved in somatic hypermutation, gene conversion, and class-switch recombination in B-lymphocytes by deaminating C to U during transcription of Ig-variable and Ig-switch region DNA. It is required for several crucial steps of B-cell terminal differentiation necessary for efficient antibody responses [4].	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	transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding RNA binding nucleic acid binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines cytidine deaminase activity hydrolase activity catalytic activity transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding RNA 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	localization transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport regulation of cellular process nuclear DNA replication localization transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport 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 cytidine to uridine editing RNA metabolic process RNA modification base conversion or substitution editing macromolecule modification 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 somatic diversification of immune receptors via somatic mutation 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 to bacterium defense response response to stress positive regulation of biological 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 DNA-templated transcription initiation regulation of gene expression positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process DNA cytosine deamination DNA deamination DNA modification regulation of single stranded viral RNA replication via double stranded DNA intermediate negative regulation of biological process viral life cycle negative regulation of single stranded viral RNA replication via double stranded DNA intermediate negative regulation of RNA biosynthetic process regulation of RNA metabolic process negative regulation of viral process viral RNA genome replication viral process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process negative regulation of viral genome replication negative regulation of metabolic process single stranded viral RNA replication via double stranded DNA intermediate regulation of viral process regulation of viral life cycle viral genome replication negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of viral genome replication negative regulation of RNA metabolic process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity immunoglobulin production involved in immunoglobulin-mediated immune response somatic cell DNA recombination B cell activation involved in immune response cell activation involved in immune response somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments leukocyte activation involved in immune response leukocyte mediated immunity lymphocyte activation involved in immune response somatic recombination of immunoglobulin genes involved in immune response immune response DNA recombination immunoglobulin mediated immune response adaptive immune response immune effector process somatic diversification of immune receptors via germline recombination within a single locus B cell mediated immunity isotype switching defense response to virus response to virus	ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex extracellular region outer membrane-bounded periplasmic space ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex extracellular region outer membrane-bounded periplasmic space cell envelope periplasmic space intracellular anatomical structure cytoplasm cytosol cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle supramolecular complex P-body membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
A [auth C], B [auth A], C [auth B]	IPR013158	Activation-induced cytidine deaminase AID	Domain
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]	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain
A [auth C], B [auth A], C [auth B]	IPR016192	APOBEC/CMP deaminase, zinc-binding	Binding 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.